"They can not seem to get the mapping correct.."
What's mapping ?
What does it have to do with the Body Shop?
Was this an insurance claim?
Does the insurance company know the roof was repaired and not replaced?
I'm not saying that the repair was not a better choice than a replacement, but the money saved could belong to the insurance company (not to put towards other things).
"Besides the mapping issues my middle seats that are supposed to fold down no longer do. They hit the back of the drivers seat (down low). "
Who's they ?
Could the repairs done on the roof have effected that?
I doubt it, but the impact from hitting a tree going backwards could have jammed something, I suppose. The seats could just be stuck. Take it back and have them show you how to fold the seats down.
Have a you got a brick and mortar insurance office with a real agent? I'd get some help there.