It depends on the size of the rust holes and the location of the holes. If its inside the bed, filling it with anything is not a good idea, the first time you put anything of heft in the bed the fill will not hold up. If its on the outside (fender) of the bed, then its better, but still not ideal. Bondo is not intended for filling large gaps. there are materials, like already mentioned, with fiberglass in them, but they are intended for very small areas. if the area is too big, I would recommend finding a bed that is not rusted out.

If you decide the area is small enough, you have to remove all paint and rust, get down to bare fresh metal. Use a wire wheel is probably your best option. Then apply your bondo/filler, you are going to want to be pretty liberal, if you have access to the back side of the metal (highly recommended, so you can make sure all rust and paint is removed), I would build up the backside pretty thick as reinforcement, and no one will ever see it. try to make the outside as smooth and as close to the trucks fender as possible, with over lap bigger than the size of the holes. this will reduce the amount of sanding required. When it is drys, sand it smooth ad flush with the fender, not removing too much of the overlap, you need this for strength. Once you have it smooth and straight, clean the surface with an acid wash (search the internet for proper cleaning prior to painting) then spray it with your primer, inside and out side, making sure to cover all exposed metal

First use a wire brush to remove as much rust as possible. The brush on rust converter. Let it dry. Then fill with bondo with fiberglass fibers. Then primer and paint

A pickup bed is made of thin sheet metal. Once it starts getting holes in it from rust you are just wasting your time trying to repair it because basically it's just shot. Go and have a new one cut out of heavier metal and fasten it in the truck.

Keep in mind that whatever you do yourself, since you seem so knowledgeable, is going to look like crap.

I have a 1970 F100 and my bed has smaller rust holes in it, so i was thinking about putting some body filler or bondo in there sanding it and spraying primer but what kind of body filler should i get? and do you think spraying it with primer will work to stop the rusting?