I don't use the truck everyday and I get standing water in the bedliner. Where do I drill holes to drain it?

 

Drain hole locations might depend on what slant is in your driveway, and whether you've leveled the rear suspension. In any case, each drilled drain hole will increase the chances of corrosion under it as not all the water will drain straight to the ground.
You might be better served by parking it where the tailgate is slightly lower than the cab - for natural drainage. Or consider purchasing and installing a tonneau cover.

 

After installing my leveling kit, I hardly get any standing water in the bed.