Use a single hitbox sprite with multiple animations (or frames). Make it the same size as your sprite, copy your sprite in, and draw over his fist or arm or whatever. Erase everything else and code it up so that when he punches it switches the animation or frame of his extra attack hitbox.
All of these things feel like work-arounds to me.
Actually, like deadeye mentioned, you're not saving much/any time with your way. Your just putting the hitbox work into the picture editor and behind the scenes of the IDE. This is worse than making a seperate sprite IMO. Fiddling with the picture editor to align frames and hitboxes is a pain as is (you can't see the hitbox during the runtime etc.), and then your stuck with a hitbox tied to your image. You won't be able to offset it for special attacks, or do other advanced things. Fighting games take a lot of work. What feels like a "work around" is actually the necessary, unavoidable work.