making a good patcher

Ok say you have to manually unpack an exe and you patch/crack it, how would you go about making a patcher for the origonal program so you dont have to distribute the patched exe?

like i unpacked somthing with aspack, but when i repack it, it messes up the icons and the size isnt near the origonal exe so ofcourse it would be very hard to find the offsets with a patcher and change them.