Should I just go ahead with a full repaint?

Thanks for the tips as this is my first vinyl top car, me being eager to find out what was under a section of the top, took a box knife and cut a square out at the seem what the bubbling is the bondo cracking and lifting from the rust, definately needs to come off now I have an idea what is happening. Sounds like I can prep and paint the roof without worrying about seeing a seem as its covered by the top, then put the glue down along with the top over the new paint.