D.W.
I would designate one as the water cup and ONLY allow water in that one. That way, you can do a quick hot water rinse before refilling. You are not supposed to store leftover drinks because kids have not mastered the total art of swallowing so there is a lot of backwash, food, etc.. back in the cup and that starts breeding bacteria quickly. I won't say that I have never done it, but usually not for more than 30 minutes.