I have been searching around different web sites trying to find a way to have multiple instances of the same emulator xboyadvance. I was trying to do this so I could have a different emulator for game boy, game boy color, and game boy advance. I figured it out and wanted to share the info in case somebody else wanted to do the same thing.
This program, xEpatcher, will change the default save directory of the emulator to be in the same folder of the emulator instead of e:\saves\xboyadvance. It patches the default.xbe by changing all instances of e:\ to d:\. You could manually hex edit the xbe file yourself, but this is easier and saves a little time. I used it for xboyadvance, but it could work with any xport emulator. Also, do not do this if you plan on running the emulator from a disc. If someone wants to know why you can't just copy the emulator to another folder, I could explain that also.
The link is
http://xbox.nugnugnug.com/xEpatcher/xEpatcher.zip