I would like to repair the usual old Ford truck rust on the bed above the wheel wells. My question is should I just bondo or put in new sheetmetal? And roughly how much would it cost to fix this?

 

Just bondoing over it will be cheap, but the rust will come back. Welding in new sheetmetal is the way to go if you're keeping the truck.
This is what bondoed over rust will look like in a few years:

 

i use to work in a body shop and if u take a wire wheel on a drill or sand blaster and bust the rust COMPLETELY OFF and get shiny metal the sand the area to be repaired with 80 grit sand paper the 180 grit and slowly feather it out as u drop grit then blow off the sanded area and wipe down really good with rubbing alcohol then useing dura glass aka kitty hair which is fiber glass resin with fiberglass hair and works like body filler (bondo) but it is 100% water proof when its cured unlike bodyfiller which will suck up water like baking soda. Duraglass does cure very very hard... like cement, so dont put on more then you need...... after a few coats and you get it sanded down where you want it a skim coat of body filler to level out the repair are and finsh off with 180 grit then a good primer over the area to give you a good foundtion to paint on.... when sanding the filler use a good stright block not just sand paper on ur hand or the repair area will wave at people whe you drive by.... i see this ALOT on backyard body jobs... if you go to a auto paint store they will be able to point you in the right direction.... the products on there shelves are going to be a bit more pricey however you get what you pay for....