I did the pure seo layout tutorial and everything was great.

Now im trying to modify the menu and nothing seems to change

the old code is

#menu
{
    position: absolute;
    top: 105px;
    left: 0px;
    background-color: #FFAE00;
    width: 100%;
    height: 32px;
}

#menu h3
{
    margin: 0;
    font-size: 80%;
    position: relative;
    top: 0;
    left: -1000px;

Then im trying to change the

Main Menu items

/* Main Menu ////////////////////////////////////////////////////////////////////////////////////////////////////*/
.MainMenu_MenuContainer
{
    border-right: #404040 0px solid;
    border-top: #ff8080 0px solid;
    background-image: url(X.Menu.BLACK.jpg);
    border-left: #ff8080 0px solid;
    border-bottom: #404040 0px solid;
    background-repeat: repeat-x;
}
.MainMenu_MenuBar {
    cursor: hand;
    height:16;
}
.MainMenu_MenuItem
{
    border-right: #000000 0px solid;
    border-top: #000000 0px solid;
    font-weight: bold;
    font-size: 9pt;
    background-image: url(X.Menu.BLACK.jpg);
    border-left: #000000 0px solid;
    cursor: hand;
    color: white;
    border-bottom: #000000 0px solid;
    background-repeat: repeat-x;
    font-style: normal;
    font-family: Arial, Helvetica;
    background-color: #000000;
}
.MainMenu_MenuIcon
{
    border-right: #000000 0px solid;
    border-top: #000000 0px solid;
    background-image: url(X.Menu.GREY.jpg);
    border-left: #000000 0px solid;
    width: 20px;
    cursor: hand;
    color: white;
    border-bottom: #000000 0px solid;
    background-repeat: repeat-x;
    height: 21px;
    background-color: #000000;
    text-align: center;
}
.MainMenu_SubMenu {
    z-index: 1000;
    cursor: hand;
    background-color: #FFFFFF;
    filter:progidXImageTransform.Microsoft.Shadow(color='#000000', Direction=135, Strength=10) ;
    border-bottom: #404040 0px solid;
    border-left: #FF8080 0px solid;
    border-top: #FF8080 0px solid;
    border-right: #404040 0px solid;
}
.MainMenu_MenuBreak
{
    border-right: #404040 0px solid;
    border-top: #ff8080 0px solid;
    background-image: url(X.Menu.GREY.jpg);
    border-left: #ff8080 0px solid;
    border-bottom: #404040 0px solid;
    background-repeat: no-repeat;
    height: 0px;
    background-color: #000000;
}
.MainMenu_MenuItemSel
{
    font-weight: bold;
    font-size: 9pt;
    background-image: url(X.Menu.RED.jpg);
    cursor: hand;
    color: #FFFFFF;
    background-repeat: repeat-x;
    font-style: normal;
    font-family: Arial, Helvetica;
    background-color: #000000;
}
.MainMenu_MenuArrow {
    font-family: webdings;
    font-size: 10pt;
    cursor: hand;
    border-right: #000000 0px solid;
    border-bottom: #000000 0px solid;
    border-top: #000000 0px solid;
    color: black;
}
.MainMenu_RootMenuArrow {
    font-family: webdings;
    font-size: 10pt;
    cursor: hand;
    color: Red;


The layout screws up and nothing changes. I even looked at the toolkit and the another layout uses a MENU token as well.

How are you "modifying the module"?

Have you learned about using Web Developers Toolbar to trouble-shoot CSS?  If not, look at Troubleshooting DotNetNuke Skins.

I use web dev toolbar all the time

The skinning toolkit has the appropiate references

and im using a simple skin lee made  with us.

Hello,

Could you zip and attach your entire skin files and I will have a look,