I throw my emulators in f:\emulators
Make a separate folder for each emulator, FTP the unzipped contents of each emulator package into that folder.
Each emulator will have a ROMs folder inside it, throw you roms in there.
See my
z26x documentation for details on installing an emulator, you'll just have to adjust the instructions slightly for different emulators. They all (at least all of xport's emulators) have the same basic layout/file structure.
you will probably have to tweak your xboxmediacenter.xml file a bit to point it to look at f:\emulators so that it shows up in "my programs" menu.
Unfortunately, I don't have my xboxmediacenter.xml handy, or I'd paste the section you need into it.
I'll try to remember to post it here, if I don't and you're still stuck, send me an email and I'll step ya through it. XBMC is a really nice dashboard, I don't understand why people don't use it.
In the mean time, you can launch emulators by going to files, navigating to the F:\emulators\whateverNameOfEmulatorYouInstalled and clicking the default.xbe file.