Best place to drill is just inside the rolled under edge of the bed/body side right where the rust always appears at the top of the wheel arches.
Just a couple of holes 1.25-1.375" diameter.
It's also a good idea to get oil up into the pinch weld periodically to keep water displaced from where it would get wicked in by capillary action, trapped and sit forever.
Doing this makes it easy to flush out and mud or salt since you don't have to pull back the plastic liners front and rear.
Jim,
Lil'Red is a '87 F250 HD, 4.10's, 1356 4x4, Zf-5, 3G, PMGR, Saginaw PS, desmogged with a Holley 80508 and Performer intake.
Too much other stuff to mention.