Hello Julien_Martin, Well why don't you put your part in mechanically welded (if it's a part), it allows you to automatically create bodies... I can't take screenshots of it because my pc is being processed... Keep us informed, good luck. @+. AR.
If you have two different sheet metal parts... Why not design two pieces? it's still easier to manage for plans etc
On the other hand, when trying to do your manipulation, I have both bodies that remain visible in my room. Can you try to tell us more about your registration procedure?