I held the flaps up to the wheel well and used a awl to punch through the flap material starting in the center and working outword. It made it easy to locate the staple holes.I use stainless steel welding rod and make my own staples(bend them with a needle nose pliers) -match the original staple holes in the inner fenders (drill them out one size larger) to fit the stainless welding rod size. I think the stainless welding rod has a 32 number on it - I can look -it comes in 2 ft sections. The staples that come with the flaps are too short with the thicknesses of the flaps and the inner fender added to together.
Also the stainless welding rod will never rust. Use small pieces of 2 by 4 and rags/towels (to not damage your inner fender paint)to bend the staples to make the staples hold the flaps really tight to the inner fenders.
You have to drill through the flaps to get the staples in the right place and "make the holes"
Paul