I had the bottom sides of the fenders sanded smooth, and added 3/16" foam padding to them to protect from stone chips "starring" the paint from the bottom side.
3M Clear Sheet on rear fender protects paint. Edge of Clear Sheet starts at upper corner of door, extends down to bottom of fenders following door cut line and goes back up at wheel opening and back across fender to corner of door. Check it out at http://www.invinca-shield.com/.