I'm only a beginner at this, but I think that it may depend on which panel you are replacing.
I butt welded my floor pan section, but it would have been a lot easier and faster to do a lap joint. As far as external panels or anything that's going to be visible, I'd only do butt welds for the reasons stated above. For a beginner like me, lap welds are far easier than butt welds when it comes to sheet metal. The thinner the joint that you are welding, the more skill it takes to do it right, IMHO.
