When you have money left at the end of a turn because you didn't have the time to spend it, it's time to auto-produce. Auto produce the units in the back of your army where you are least focused first (So you aren't limiting what units you are using in the front lines). I almost always set it so that it's not automatically done then i can decide how much money i get. Exempt port cities from auto-produce since it will help you move the units around much faster.