The roof on my bus was painted 12 years ago with 2 stage paint. I could tell as soon as I got the bus back from the painter that they really cut corners and put a thin layer of paint and clear coat on the roof, which did not hold up as long as the sides of the bus. Now I am in the same boat as you-- having to sand and scape the peeling paint. I am just going to sand and prime, then put a coat of one stage paint. It should last longer than me.
BTW, if the paint bubbles, it means poor surface preparation. I also have a few spot on the sides I am having to repaint because of bubbles and peeling clear coat.