I have 8 schools right now in my UP game, having captured a few later on in the game. I'm up to 22 provinces now out of 40 needed. All of my colleges are in different provinces. Some of them I built in small provinces with not much else. Mines and towns increase unhappiness so if you build a college in a province with almost nothing else, you won't have a huge amount of unhappiness in that town. Also, you can exempt it from taxes since it generates barely anything anyway.

Keep an eye on your ministers as well. They get negative traits to happiness from time to time. Just kick those ministers out. Chances are, the ones replacing them will have no traits.