I notice that loops on the sides of the bed pretty much don't help me tie anything *down* into the bed.

So I did almost exactly that - except I drilled 8 holes in the bed floor and put eye bolts in 'em. 2 at the front, 2 just ahead of the wheel wells, 2 just behind the wheel wells, and 2 at the back. I sealed 'em with silicon and when it rains, my truck bed still holds water if it's parked facing downhill and water can't drain out the back.

EyeBolt - Fender - nut - truck bed, Fender - lockwasher - nut.

Caveat: as always - when you're drilling holes in your truck be sure you find what's on the other side of the hole, so you don't, say, drill into you gas tank or something.