I know how important the floor is for structure for these unibody cars... so to get even a bit more penetrationinto the rails and rockers (which are WAY thicker than the floor) I would use a drill and slightly drill into them so as to get deeper penetration! Might be overkill, but makes me feel better.
Then I just turned up the HEAT!! welding them as hot as I could to get as flat of a plug weld as I could.