Go into the ggpo installation folder, and open up the final burn alpha emulator (has a funky name in that folder), then load your rom, and then go to Game>Map Game Inputs, then after you setup your controls for that game (you have to do it for every game), go to Misc> Save Mapping inputs.
Edit: beated
What they said.
Cheezy, make sure the zipped rom is in the roms folder.
That new video converter worked fine, but you can only do one at a time. So I copied the settings back over to Total Video Converter. The correct format is H.264 480x320
I can do a whole folder that way.