Bed Rust Repair
A couple pics of the extent of the rust would help us to help you. One of the entire box, and another of a closeup of the worst area. The reality is though, you need to eliminate the rust before covering the bed.
If the rust spots aren't holes you should be ok just sand blasting them and putting some self etching primer over them. If they are holes (moisture can get to them from the other side of the panel through the hole) you'll have to cut them out and patch them correctly before you do the liner. Even if they're only pin-holes you'll have issues fast.
For prepping for the liner? I would use a red scotch-brite pad. From a body supply store. not something for washing dishes. Red pads are really aggressive and can bend into the corners of the bed. An 8 foot bed you could do in four pads.
The bed is bare metal? You cannot leave metal bare for very long. Pics of the rust please, and we can get you on your way. All you need is one humid day, and the rust will begin. You need to get that project started NOW. Bare metal is nothing to let sit around. Take a picture, and post it. If it has been sitting bare for a while, your best option is to take it to a sandblasting place near you, and have it blasted. Then IMMEDIATELY get it primed, then bed lined. Pics are the only way we can guide you. There are too many "what if's" without them.


