My Subs??

I got a set up of 3 Rockford Fosgate Series 1 with a custom box from your heard to the back where the amps are placed. the prob is I have blown my rear windshield out of place. I've been told told many things to do what is the best. also my paint job was losing the clear coat a long time ago well now that I got my system I have seen what looks to be like water underneath the paint like bumps. is this from the system making hte roof flex so much up and down or should that not affect anything?Thanks 40oz.