remove the stuff you want painted, much easier to remove completely than tape and plastic bag the whole area you dont want sprayed. Plus removing them will also allow you to hit the entire fender and get all the mud and dirty/ sand and debris that was stuck between the fender and body.
Sand the old paint off of the fender, it doesnt have to be perfect, but enough to get a good bond. Then wipe the fenders down and you can do one of two things. buy the primer and apply that before the truck berliner, or you can just skip the step and go straight to the bedliner. All depends on preference. I actually skipped it and went right to the bedliner because i know its going to get scratched up and i can just spray the scratches. And as for clear coat, you can do it to make it shine, but scuffs and scratches will show more and when you have to fix it, you cant just bedline it, you need to sand, bedline and then clear coat again.
good luck and i hope this was helpful.