I use a product called Rust-Mort that converts the rust, then I POR15 if its a frame, or prime and paint if its a body panel.
POR15 is actually supposed to adhere better if you leave the (not loose) rust in place. I did their 3-step process to a machete which I routinely use during the summer months at my folks' cabin for gathering firewood and its held up extremely well over the course of about 5 years. Literally the only place where the POR15 has come off is where I have used a bastard file (right along the edge) to sharpen it a couple times!
2011 F150 5.0L 4x4
1996 Mustang GT 5spd - PI Cams and intake, Bassani OR X pipe, Dynomax Ultraflow mufflers, C&L plenum with 75mm TB, K&N FIPK, Hella FF75 foglamps, Cobra "Terminator" convertible top.