[Morkilus]

I'm a relatively new player, but I think I can answer most of your questions. Also, the search engine in the forum is pretty robust (helps if you put a plus sign in each term if you have multiple terms).

1. Yes, both commanders and units gain XP and stats with XP. If your commanders are among the deadliest, they get into the Hall of Fame and get special powers.
2. Fortresses "gather" resources and taxes from immediately surrounding territories, so it's good to build them next to mountains and forests if you want to build lots of national troops with high resource costs. They also protect your temples and groups of high-value commanders such as sages, so build them where you have temples and libraries. Any commander can resume building a fort, so you might as well have a cheap one build it. You can switch them off, only one commander is needed to build it.
3. It's up to you... in multiplayer, it's better to make alliances and non-aggression pacts rather than spread your armies about. The AI can be intimidated by large groups of militia, most humans aren't.
4. The skill is refering to your path level... there are no magic sites to be found with path level greater than four, so if your 4e4n Earth Mother can't find anything, there aren't any Earth or Nature sites to be found in that province. Most players like to use site-searching spells from a distance, like Haruspex and Earth Lore.

Have fun