Well, I just had my car in to have the windshield sealed, because it was leaking badly. They did it from the inside and used a thick substance (I know what it is but since I cant spell it O_o) and it is keeping the water from entering the car....

The thing is, though, the windshield is still out of alignment (due to an accident I was in) and when i wash my car I can still see water going into the gap between the roof and the windshield.

Is water going to sit in there and rust out the roof of my car, or will the water seep out somplace else since it can no longer get to my interior?

 

I would see if it can be sealed on the outside. THe water has got to go somewhere, and if you don't know where it is going it is hard to know if it is somewhere it would rust.