Do not use Bondo to "build structure or do fitting such as bottom metal or correcting a larger flaw. For that a simple fiberglass (automotive) kit with matting not cloth will allow you to build up surfaces as needed to correct structure flaws.. Cloth can give a very finished surface if needed though. It sounds like you have some low spots in some areas that need to be brought up. After you have all contours and shaping done within a few mils and pillars and all metal test fitted but not final bedded you can use a Bondo skim coat to fill small imperfections that fiberglass is famous for or feather fill which is a high build primer made for fiberglass. Prime and paint as desired then finish bedding with preferred material (Acraglas. Steelbed, etc...) Some prefer to bed first then paint with appropriate masking. Good luck with this...
