Hi Matt,
I'm not sure I would have picked the IBuySpy Skin as a starting point, but in any case the menu css is in the stylemenu.css file in the skin folder. Make sure you work first in Firefox, don't design using IE, get it right in FF first then override things as needed to fix any IE funkiness using the IESpecific.css and IE7Specific.css files. If you are making a change in stylemenu.css and are using IE you may not see any change because the setting in the IE specific file is overriding the main style.
The css files are organised in a modular fashion to make it easier to find things. Most of the css class names are the same in all skins and just their values are different. style.css includes the other files, things that affect layout, ie height width margins positioning are in stylelayout.css, font styling is in styletext.css, colors are in stylecolors.css, background images are set in styleimages.css, its really straightforward actually and allows you to change colors without changing layout or layout without changing colors etc. Some feature specific css files are only loaded as needed to keep the page lighter weight. styletreeview.css for example is only included if you are using the treeview menu.
See the documentation here:
http://www.mojoportal.com/creatingskins.aspx
Hope it helps,
Joe