Figured it out! Yay!
Turns out I actually changed too much of the CSS. I had changed things from "nav" to "menu" but inadvertently changed one of the "navwrap" styles as well. In style.css, on line 895, I needed to keep the .navwrap that contained the positioning. I changed it back and now we're good to go.
So, if anyone is looking for the steps to do it themselves...
-Start with Justin Tadlock's tutorial for the basics:
http://justintadlock.com/archives/2010/06/01/goodbye-headaches-hello-menus
-Add the new functions to functions.php
-Change list_pages to the new nav_menu tag in your header.php
-Update style.css, in the navigation section, all the "#top #nav" styles to ".menu"
-Update the similar sections in the style#.css file you're using in the same manner.
The code I used is below, in case anyone finds it helpful.
header.php
<div class="navwrap">
<ul id="menu">
<?php wp_nav_menu(); ?>
</div>
functions.php
// New WP3.0 Menu
add_action( 'init', 'register_my_menus' );
function register_my_menus() {
register_nav_menus(
array(
'primary-menu' => __( 'Primary Menu' ),
'secondary-menu' => __( 'Secondary Menu' ),
'tertiary-menu' => __( 'Tertiary Menu' )
)
);
}
style.css
.navwrap{
font-size:12px;
height:50px;
right: 5px;
line-height:50px;
padding-right:18px;
position:absolute;
top:32px;
z-index:6;
}
.menu{
float:left;
height:50px;
line-height:50px;
padding-left:13px;
}
.menu ul{
margin:0;
padding:0;
list-style-type:none;
list-style-position:outside;
position:relative;
line-height:50px;
z-index:5;
list-style-image: none;
}
.menu a{
height:33px;
display:block;
padding:0 21px;
text-decoration:none;
text-align:center;
line-height:28px;
outline:none;
z-index:35;
position:relative;
float:left;
}
.menu ul a{
line-height:33px;
list-style-image: none;
}
.menu li{
float:left;
position:relative;
z-index:20;
margin-top:11px;
list-style-image: none;
}
.menu li li{
border-left:none;
margin-top:0;
list-style-image: none;
}
.menu ul {
position:absolute;
display:none;
width:202px;
top:33px;
left:-1px;
list-style-image: none;
}
.menu li ul a{
width:160px;
height:auto;
float:left;
text-align:left;
padding:0 21px;
list-style-image: none;
}
.menu ul ul{
top:auto;
border-top:none;
list-style-image: none;
}
.menu li ul ul {
left:202px;
top:0px;
list-style-image: none;
}
.menu li:hover ul ul, .menu li:hover ul ul ul,.menu li:hover ul ul ul ul{
display:none;
list-style-image: none;
}
.menu li:hover ul, .menu li li:hover ul, .menu li li li:hover ul, .menu li li li li:hover ul{
display:block;
list-style-image: none;
}
style5.css
/*navigation*/
.navwrap{
background:transparent url(../images5/menu.png) no-repeat scroll right bottom;
}
.menu a{
color: #9f9f9f;
}
.menu ul {
border:1px solid #DFDFDF;
border-top:none;
}
.menu li ul a{
border-bottom:1px solid #fff;
border-top:1px solid #DFDFDF;
}
.menu ul a, .menu ul li{
background-color:#fff;
background-image:none;
}
.menu ul a:hover, .menu ul a:focus {
background-color: #3b5987;
color:#fff;
}
.menu a:hover, .menu a:focus {
color: #fff;
}
.menu{
background:transparent url(../images5/menu.png) left top no-repeat;
}
Some of that is probably redundant, but who knows, someone might find it handy.