I would say you are best to just mix it up. You definitely don't want to shoot too much after doing an upper body workout. If you are shaky and having a hard time holding on target all you are going to do is develop bad habits like punching the trigger. Also if your arms / shoulders are tired and you are having a hard time pulling the bow back you'll develop bad habits there as well.
Shooting 12 good arrows is way better than shooting 40 bad ones. Always practice good form and shot execution and you'll become a better shot.