Exactly. Most of the animal alliance locations will be the smaller settlements.

I said 1,000s of years in my first post, but that may or may not be too long. It did take the humans back down to caveman level at the start so they had to work their way back up to medieval after all this time and all the animals had to settle in with their new abilities and build cities/form alliances. That would take at least a couple hundred years.