Welcome to CHR

Yes you should use skim filler for the pits. Be sure you work it into the hole though, otherwise it will just cover the pit and not fill it. Also you should put a thin coat over the entire area you're working on, this will help prevent waving in your panel.

Body filler works just fine for straightening surfaces. Metal 2 metal is great stuff if it's on bare metal. BONDO is a brand name, I use evercoat filler. It hasn't failed me yet.

Good luck and drop us a line if you have more questions.

Oz