Have you trial fitted it onto the car?I replaced a patch panel area on the rear quarter with no problem.
You need to cut the patch panel you bought to the contour of the area you want replaced.
Before doing that, clamp it and/or screw it (perimeters) onto the original thats still on the car.
Make sure its perfectly overlapped and hugging the original sheet metal contours you are wanting to replace. There should be no air gaps. It should be almost as though it was part of the car.
Now you are ready to cut thru both at the same time.
Cut right thru both at the same time just above the area you desire replacement. I used a 3 inch metal cut off wheels.
http://www.harborfreight.com/pack-of-10-3-inch-cut-off-wheels-for-metal-44812.htmlAlign the new portion into place where the one behind you just cut out was. Again use small clamps if necessary to put into correct placement.
Now it is ready to mig weld into place. One small spot at a time alternating locations. This is important. you don't want sheet metal to accumulate too much heat or it'll warp.
Then grind off the weld head beads.
If it still doesn't seem right then you didn't evaluate the metal contours prior to fitment.