My name is XXXXX XXXXX X will be helping you today. Most questions will involve troubleshooting, and usually take many posts back and forth. Post back with questions as needed.
There are different grades of "fillers" out there. The fillers made by Bondo are not very good. There are other brands out there such as West System, US Chemical, Evercoat, that are very good.
What you want to do, or try to do, is build up your actual fiberglass laminate with mat and resin the best you can so that when it does come time to smooth it over, you do not have a glob of filler that is 1/2 an inch deep. Try to keep your filler under an 1/8th of an inch thick if possible. But definitely no thicker than 1/4 inch deep. If you try to glob filler into voids it is just going to crack and fall out over time.
If this was my repair I would build up my mat laminate first, smooth it over with a high quality filler (not bondo - Personally I use fillers made by US Chemical). I would gel-coat it as that will add water protection. Fillers, paints, and even fiberglass are not totally water proof. Filler is definitly not water proof. And then after the gelcoat sand it down and bottom paint.
Feel free to post back with any questions