I assume you bought the patches that go along the bottom, from the front of the door to the front wheel opening? Once installed, they will have a slight curvature, giving the side of the car a bit of a boat shape. Being flat is not a problem, as the curvature is in a single direction, and not very pronounced. You will have to mark where to cut the old fender, using the new patch. Then cut off the old and weld in the new patch.
What type welder are you using?