Foam seems like more trouble than its worth. Me method of gluing the cotton fleece to the sides and glassing it for a shape was pretty easy and painless..
As far as bondo, use sanding blocks, and never bondo over bondo that hasnt been sanded. Meaning make the bondo as flat as possible before adding another layer. Use lightweight bondo on smaller areas that have a lot of details (the notches on the sides of the amps on my box). Always mix only as much as you can use, and the smoother you lay it the easier it is to sand it and the less waste you have. I use the bondo brand "squeegy" things. Those are nice because they are the pinkish color that is reccomended when mixing the bondo.
Use thinner to clean the squeegy, if you dont have any, what works is to put the leftover crusty bondo in a pile on wherever you mix it, and push one side of the squeegy down on it. Once its hardened you pull it off and that half of the squeegy is perfectly clean. You dont want junk stuck on it making lines in your bondo when you put it down.
And for pits, use that tube of pre-mixed bondo. Its that red stuff that you just put on with your finger in the small pits and it hardens by itself. Use that only for filling pits, not to shape anything.
I didnt use any bondoglass. Just bondo, and the lightweight stuff.
When primering, first put a coat or two of a single color primer, then wetsand all the way to the bondo with medium-fine sand paper. That will fill all the lines from sanding with the heavy duty sand paper. Then what I would do is spray 2 coats of a light color primer, and two coats of a dark color primer. Wet sand with a wetsanding block (somewhat flxible sanding block). If you have an area that stays the darker color, you have a large indention or pit there because the sanding block isnt flush with the shape of the box. Make sence? basically its a way to bring out the imperfections that you cant see when the box is a flat color, and all the same color. If you were to paint and clearcoar over that large dip, it would be visible when the light hits it.