this is the front wheel liner without the flaps installed. you see the raised part of the liner about even with where the flare ends?
Here's the flaps installed up front, you can see that the flaps are about even with where that raised section of the wheel liner is. If I didn't cut the flaps they would sit a little cocked being overlapped. Cut around it they now sit nice and flush with the fender flare plastics. The other thing you could do is just install the flap down lower like some guys have done, but you're reducing ground clearance and the flaps may rub on stuff. Up front that is a concern just using self tappers in plastic. And also with them sitting lower they stand out more flapping in the breeze more. With where mine are, 12" off the ground, even hitting mud puddles they still sit low enough that it keeps ALL crap from being slung on the paint, yet still high enough they aren't standing out or dragging on anything offroading.