As far as the two tone paint goes, either pinstripes or bury the seam in the clearcoat.

I suspect most patch panel jobs like you mentioned were not properly coated on the back side after the job was done. The weld burns away whatever factory coating was there and the rust starts all over again. Use some weld through zinc primer to spray on the back side of the areas you will be welding prior to welding it. Get yourself a spray wand to stick in between the inner and outer bedside and go to town after welding spraying some rustproofing in there.

Make sure any bondo you use is on top of epoxy primer. It will cause bare metal to rust especially if it is allowed to get wet before painting.
It also needs at least a primer sealer coat on top to sandwich it in between. Hope this helps.