Your 3S and 2S pack probably need to be the same C rating and capacity though to work best and to avoid having issues. It might work, but for instance running a 20C 2S with a 40C 3S is probably a bad idea. As would be running a 7200mah 2S and a 5000mah 3S.
Having different capacities would probably work ok as long as you have the alarms on both packs and you stop when any of the cells get too low. But I have to assume running different C rating packs may not be a great idea.
Having different capacities would probably work ok as long as you have the alarms on both packs and you stop when any of the cells get too low. But I have to assume running different C rating packs may not be a great idea.