Okay, so today we had a problem with the computer. After getting it fixed, or fixing it actually, I did that. I started moving things out of the backup folder into where they belong. I did some more stuff to my map, and then went to munge it. It asked me the game directory, and I clicked on program files/lucasarts and left it at that. Now when it munges, the map goes to an addon folder that it created right inside the directory, not gamedata. Is there a way to fix that without reinstalling the modtools?

Click on the VisualMunge.exe and select "Options" at the top of the toolbar, then click on Set BF2 Directory, then browse to the location of your "Gamedata" folder.

Okay, thanks.