Rance,
Depending on what you want to do with your truck, if the pits are surface only and the steel has good integrity, there is nothing wrong with using a little body filler in the pits.
Just be patient enough to go all the way down (high numbers, e.g. 600) with your sanding. It is amazing how body filler that feels perfect under your fingers can still look like crap with a coat of paint on.
