I want to add my emulators in the XBMC "programs" tab. seems like every time I try the add source, I get all the files in there and never the shortcut.

Where are your emulators? If they're in F:/Emulators then setting that folder as a source should work, and also mean that skins with an emulators link will take you straight to them.

Yes they are. But when I link to that folder. The it shows all the coinops folders. Not just the game link.

looks like you added the contents of coinops folder to emualtors....make a folder called coinops or arcades or something and place all the files in that

It also sounds like you might have not added the source correctly. When in xbmc open the programs menu and press the white button on the controller and that will bring up and options screen that give you the option to "add source".
Just point it to F:Emulators or E:emulators and that should do the trick. Also, make sure you get a good icon for it

Sounds about right !
Each emulator needs to in its own folder within the emulators/games directory to achieve what your after.

Yep that did the trick. Thanks guys