How would you drilled holes in the bed?

Previous owner drilled holes into the wheel wells in the bed and kinda deformed one of them with the metal protruding out a bit more than the rest.

I plan on using some JB weld to fill the holes then get it sprayed with bed liner. But wondering if that one that’s protruding a bit more due to the pressure of a drill being pressed from the opposite side will stand out too much?

 

It will be noticeable. I'd take a section of 2x4, put an end on the protruding offending bump and wack the other end with a mallet. It will straighten the bump out enough before spraying. Just take it slow and you'll be able to straighten it out.

 

This.