Новое меню перекрывает старое

я думаю стоит смотреть в сторону внутренних-внешних отступов. Если они будут нулевые, то блок теоретически встанет туда куда нужно.

А эти отступы нужно менять в файле style.css?

Их нужно менять в том файле, который за них отвечает. Чаще всего это style.css

наиши, что у тя в style.css

/*
Theme Name: Cloudy
Theme URI:
Description: WP Cloudy theme designed by <a href="http://www.aoemedia.de">AOE media GmbH</a>. Cloudy is a beautiful simple blog theme, designed for commercial and more technical blogs. Now also widget ready.
Version: 1.63
Author: AOE media GmbH
Author URI: http://www.aoemedia.de
Tags: two-columns, fixed-width, blue, custom-header
By downloading and using this theme, you agree to the following terms:
– All variations of this theme have to remain GPL
– You may use this theme for personal or commercial projects
– You may modify, translate or distribute

For support requests please contact: wordpress(at)aoemedia.com. Requests through other channels (website etc.) can unfortunately not be responded to.

*/

/* Reset styles
*******************************/
html, body, div, span,iframe,
h1, h2, h3, h4, h5, h6, p, blockquote, pre,
a, abbr, acronym, address, cite, code,
del, dfn, em, font, ins,strong,ol, ul, li,
fieldset, form, label, legend,
table, caption, tbody, tfoot, thead, tr, th, td {
margin: 0;
padding: 0;
border: 0;
outline: 0;
font-weight: inherit;
font-style: inherit;
font-size: 100%;
font-family: inherit;
vertical-align: baseline;
}
:focus {
outline: 0;
}
body {
line-height: 1;
color: black;
background: white;
}
ol, ul {
list-style: none;
}
table {
border-collapse: collapse;
border-spacing: 0;
}
caption, th, td {
text-align: left;
font-weight: normal;
}

/* Main styles
*******************************/
html {
height: 100%;
margin-bottom: 1px;/* force vertical scrollbars */
}

body {
background:url(img/body.jpg) 0 0 repeat #dff4ff;
color: #646464;
font-size: 75%;
text-align: left;
}

/* Default fonts
*******************************/
body,
input,
select { font-family: Tahoma, Arial, Helvetica, sans-serif; }
textarea,
pre,
code { font-family:"Courier New", Courier, monospace; }

/* Header elements
*******************************/
h1,
h2,
h3,
h4,
h5,
h6 {
font-weight:normal;
font-family: Tahoma, Arial, Helvetica, sans-serif;
}

h1 {
font-size: 2.5em;
color:#fff;
line-height:1;
}
h2 {
font-size: 1.5em;
}

h3 {
font-size: 1.5em;
padding-bottom:1em;
color:#518cb1;
}
h4 { font-size: 1.3em; }
h5 { font-size: 1.2em; }
h6 { font-size: 1.1em; }

/* Text elements
*******************************/
p { margin: 0 0 1em 0; text-align: left; line-height:1.2; }
p.last { margin-bottom:0; }
p.first { margin-top:1em; }
p.img { float: left; margin:0 1em 1em 0; padding:0; }

blockquote {
margin:0 0 1em 1em;
padding-left:1em;
border-left:2px solid #B8E0FA;
}
strong { font-weight: bold; }
em { font-style: italic; }
pre { border: 1px solid #ddd; margin-bottom: 1.2em; padding:1.2em; }
ins { text-decoration:none; } /*remove underline from text*/
del { text-decoration:line-through; }

dl {
line-height:1.2;
margin-bottom:1.2em;
}

hr {
color: #fff;
background:transparent;
margin: 0 0 0.5em 0;
padding: 0 0 0.5em 0;
border:0;
border-bottom: 1px #000 dotted;
}

/*links*/
a:link,
a:visited,
a:focus,
a:hover,
a:active { color: #518cb1; text-decoration: underline; cursor:pointer; }

a:hover {}
a:visited {}

a:active,
a:focus { outline: 0; } /*remove border in ff*/

/* decorate lists in posts */
#content .post ul,
#content .post ol {
margin: 0 0 1em 2em;
}

#content .post ul {
list-style-type:disc;
}

#content .post ol {
list-style-type:decimal;
}

#content .post ul li,
#content .post ol li {
line-height:2;
}

/* Images
*******************************/
img { outline:0;border:0; }

/* Form styles
*******************************/
input,
select,
textarea {
font-size:1.0em;/*by default font-size is bigger*/
vertical-align:baseline;
}

input.text,
input.file { cursor:text; }

input.button {
cursor:pointer;
color:#fefefe;
border:0;
background:url(img/header-search-button.gif) 0 0 repeat-x;
font-weight:bold;
padding:1px 12px;
text-align:center;
height:19px;
}

input.radio,
input.checkbox { border: 0;padding: 0; }

/* WordPress aligning
*******************************/
.aligncenter,
div.aligncenter {
display: block;
margin-left: auto;
margin-right: auto;
}

.alignleft {
float:left;
margin: 0 1em 1em 0;
}

.alignright {
float: right;
margin: 0 0 1em 1em;
}

.wp-caption img {
margin: 0;
padding: 0;
border: 0 none;
}

.wp-caption {
border:1px solid #eee;
text-align:center;
padding-top:4px;
}
.wp-caption p.wp-caption-text {
font-size:.92em;
text-align:center;
}

/* Text align
*******************************/
.t-right { text-align: right; }
.t-left { text-align: left; }
.t-center { text-align: center; }
.t-justify { text-align: justify; }

/* Other
*******************************/
.clear:after {
content: ".";
display: block;
height: 0;
clear: both;
visibility: hidden
}

.zoom {
overflow:hidden;
}

/* Main styles
*******************************/
#root {
width: 980px;
margin: 24px auto 0 auto;
padding-bottom: 24px;
}

/* Header
*******************************/
#header {
overflow: hidden;
}

#header .menu,
#header .search {
background:url(img/header-menu-back.gif) 0 0 repeat-x #5B94BE;
}

#header .menu {
float:left;
width:667px;
height:28px;
padding:10px 20px;
}

#header .menu li {
float:left;
background:url(img/header-menu-delim.gif) 100% 0 no-repeat;
}

#header .menu li.last {
background:none;
}

#header .menu a {
color:#fefefe;
font-weight:bold;
padding:0 14px;
display:block;
line-height:2.2;
}

#header .menu a:hover {
text-decoration:none;
}

#header .search {
width:236px;
height:20px;
float:right;
padding:14px 16px;
font-size:0.92em;
}

#header .search label {
color:#fff;
padding-right:8px;
}

#header .search input.text {
width:122px;
border:1px solid #5286ab;
border-right:0;
border-bottom:0;
background:#ecf0f2;
padding:2px;
color:#34668a;
margin-right:8px;
}

#header .search input.button {
color:#fefefe;
border:0;
background:url(img/header-search-button.gif) 0 0 repeat-x;
font-weight:bold;
width:51px;
padding:1px 0;
text-align:center;
height:19px;
}

#heading {
margin-top:4px;
width:551px;
float:left;
clear:both;
height:134px;
background:url(img/heading.jpg) 0 0 no-repeat;
padding: 66px 0 0 156px;
}

#heading a {
color:#fff;
text-decoration:none;
}

#heading .description {
color:#fff;
}

#about {
margin-top:4px;
width:232px;
height:164px;
overflow:hidden;
float:right;
background:url(img/header-about-back.gif) 0 0 repeat-y #f9fdff;
padding:18px;
}

#about .signature {
text-align:right;
margin:0;
}

#main {
margin-top:4px;
clear:both;
overflow:hidden;
}

#left-block {
width:216px;
float:left;
}

#left-block .box {
background:#fff;
padding:18px;
margin-bottom:4px;
}

#left-block .box h2 {
padding-bottom:16px;
}

#left-block .box ul {
font-size:1.17em;
}

#left-block .box ul.children {
padding-top:8px;
font-size:1em;
}

#left-block .box li {
padding:4px 0;
padding-left:20px;
background-repeat:no-repeat;
background-position:0 6px;
background-image:url(img/cat.gif);
}

#left-block .box li.current-cat {
font-weight:bold;
}

#left-block .categories li {

}

#left-block .archive li {
background-image:url(img/cal.gif);
}

#left-block .blogroll li,
#left-block .meta li {
background-image:url(img/arrow.gif);
}

.box input.text {
border:1px solid #5286ab;
border-right:0;
border-bottom:0;
background:#ecf0f2;
padding:2px;
color:#34668a;
width:110px;
font-size:.92em;
}

.box input.button {
font-size:.92em;
width:48px;
}

.box .tags {
line-height:1.4;
}

.box .textwidget {
font-size:.92em;
line-height:1.4;
}

#left-block #recentcomments {
font-size:.92em;
}

#left-block #recentcomments li {
background:none;
padding-left:0;
}

#wp-calendar {
width:180px;
font-size:.92em;
}

#wp-calendar caption {
padding:0 0 4px 0;
font-weight:bold;
}

#wp-calendar th,
#wp-calendar td {
padding:2px;
text-align:center;
}

#wp-calendar thead th {
background:#eee;
}

#wp-calendar #prev {
text-align:left;
padding-top:4px;
}

#wp-calendar #next {
text-align:right;
padding-top:4px;
}

/* Content
*******************************/
#main-block {
width:760px;
float:right;
}

#content {
padding:18px;
background:#fff;
min-height:400px;
height:auto!important;
height:400px;
}

#content .post {
overflow:hidden;
margin-bottom:18px;
clear:both;
}

#content .entry a {
color:#e08105;
}

#content .date {
float:left;
width:54px;
height:43px;
padding-top:11px;
background:url(img/post-date.gif) 0 0 no-repeat;
color:#669abb;
font-size:1.67em;
text-align:center;
margin: 0 0 20px 0;
text-transform:uppercase;
}

#content .date span {
font-size:0.65em;
display:block;
}

#content .title,
#content .postdata {
margin-left:74px;
}

#content .page .title {
margin-left:0;
}

#content .title h2 {
background:url(img/post-title-border.gif) 0 100% repeat-x;
padding-bottom:8px;
margin-bottom:8px;
}

#content .title a {
text-decoration:none;
color:#265a8b;
}

#content .title a:hover {
color:#518cb1;
}

#content .postdata {
font-size:0.92em;
}

#content .category {
background:url(img/cat.gif) 0 1px no-repeat;
padding-bottom:1px;
padding-left:20px;
float: left;
}

#content .comments {
background:url(img/comment.gif) 0 1px no-repeat;
padding-bottom:1px;
padding-left:20px;
float: right;
}

#content .category,
#content .category a {
color:#91adc1;
}

#content .entry {
clear:both;
}

#content .entry .more-link {
font-weight:bold;
color:#518cb1;
}

#recent {
margin-top:4px;
background:#e7f5fe;
overflow:hidden;
}

#recent .posts,
#recent .comments {
width:312px;
padding:24px 32px;
}

#recent .posts {
float:left;
}

#recent .comments {
float:right;
}

#recent .posts ul,
#recent .comments ul {
font-size:.92em;
line-height:1.2;
}

#recent .posts li,
#recent .comments li {
margin-bottom:1.1em;
}

#recent .posts li a {
font-weight:bold;
}

#recent .comments li .author {
font-size:0.91em;
line-height:1.4;
}

#recent .comments li a {
text-decoration:none;
}

#leavecomment {
padding-top:1em;
}

.comments-list .avatar {
margin-bottom:4px;
}

.comments-list li {
padding:18px;
line-height:1.2;
}

.comments-list li.graybox {
background:#f5f5f5;
}

.comments-list cite {
font-weight:bold;
font-style:normal;
}

.comments-list small {
font-size:.83em;
}

.comments-list .comment {
margin-top:8px;
}

#commentform input.text,
#commentform textarea {
border:1px solid #5286ab;
border-right:0;
border-bottom:0;
background:#ecf0f2;
padding:2px;
color:#34668a;
}

#commentform input.text {
width:200px;
}

#commentform textarea {
width:600px;
}

/* Footer
*******************************/
#footer {
margin-top:4px;
padding:4px 32px;
font-size:.92em;
overflow:auto;
line-height:1.2;
background:url(img/cubes.gif) 705px 4px no-repeat;
}

#footer img {
vertical-align:middle;
}

#footer .copyright {
float:left;
}

#footer .links {
float:right;
}

#footer .links a {
padding-left:16px;
margin-left:16px;
background-repeat:no-repeat;
background-position:0 1px;
}

#footer .rss {
background-image:url(img/rss.gif);
}

#footer .login {
background-image:url(img/login.gif);
}

#footer a.powered {
padding:0;
}

это все style.css

Не пойму зачем нужно было просить выложить весь css целиком, достаточно было только фрагмент содержащий свойства для .menu Ну да ладно. Похоже вся проблема в этих строках:

#header .menu {
    float:left;
    width:667px;
    height:28px;
    padding:10px 20px;
    }

замените на:

#header .menu {
    float:left;
    width:667px;
    height:28px;
    padding:0;
    }

Спасибо огромное, все получилось! помогло