I bought a 92 hatch with a gsr swap in it and currently the shell is completly gutted and the dmg on the rear passenger side was bondoed over.. it looks good but in some spots is VERY thin, and has cracked so it formed a leak. I was curious as to what i should do. Maybe just bondo from the inside? and if so.. any certain brand or type i should use?

Ill try and get pics asap.

 

The cracks are not from being very thin. Most likely it is from being too thick. You should not be able to put filler on from the inside since there should be metal underneath anything that was mudded up.
The only fix is to grind it all off. See what you are working with and eather bang it out more and mudd it up again, or replace the panel.