Paint over Bondo

I have a truck hood and top off a 1989 truck my kids bought that looks like a Cheetah scratched it. A MoPar parts guy suggested I use OSPHO, after sanding just as extra rust insurance. I used epoxy primer before a bondo with aluminum. Next I used primer. I'm finished painting, but there are high and low areas from some views, that seemed to appear after I finished. It's a 20 foot paint job for sure, but I feel the body is protected. Any advice for next time?