You can do this with the 'rename dirs' option. If you are using GoodWindows as a frontend, just tick that box and your roms will be separated into folders like you want.
Unfortunately, GoodGBA is getting very outdated, so many entries are wrong, so do not delete your roms just yet if they are marked as 'bad'. However, Cowering aims to release updated versions of his tools before Christmas.
I recommend that you have a look at the latest No-Intro dat, which you can use to verify roms that GoodGBA doesn't have in the database:
http://www.gbadat.altervista.org/index.htm