Jake,
You can use everything you mentioned ... bondo, short strand filler (duraglass), and matt. Its all polyester based and its all compatible with gel. Like anything else, the amount of "filling" i.e. thickness should determine what type of material to use.
If you do a search on the fourms for "How to blueprint boat bottoms" you should find a thread with step by step instructions by Jeff Bennet.
Good Luck!
Corey