1. What happens to the populations that lose a combat? Do they leave the game, go back to the well of souls? Back to the well of souls. There are cards that can allow you to permanently reduce the population potential of a race by removing a token from the game, but they say so explicitly.
2. Can more then one population token occupy the same territory? No.
3. When you take over a territory I take it you are suppose to populate it with a token from the well of souls right? Yes.