The bed gets used. Sometimes bricks, sometimes metal, sometimes I shovel stuff from it. The rest of the time it sits outside.

What's the best way to deal with rust spots? Sand, clean, prime, touchup paint, or sand and use white herculiner.

98 GMC 2500HD, if it matters.

 

You could do a spray in bedliner. Even then I'd recommend a bed mat. Or you could just do a bed mat. If you don't do a spray in liner you will need to clean and paint the rust spots.

 

Sand paper, Grind or sand blast. Do what ever you need to do to remove the existing rust to prevent it front growing. Cover it with a rust inhibiting paint and primer.
Allow for cure time (as per instructions on can)

Sounds like you use your truck like a truck should be used. So I would spend the cash for a good reputable truck box bed liner.

My opinion
I like removable bed liners like my Duriliner
I get my truck oil sprayed every year to protect from rust. To avoid oil on my bed liner, I remove it during the spraying process