Lastly, essence - do you get one per level of the city or something like that?
No you don't, not unless its specific to the campaign.
So: Is permanently actually permanently or does it work the same way as enchantment maintenance, and disappears once the creature dies?
I think its permanent, I wont touch it.
Also, I am slightly unsure of how you learn spells. I've noticed that with fireballs, for instance, I get a strategic spell that lets a champion cast fireball, but they also get fireball as a fire mage? Does anything need to be researched for that?
You get spells from 2 sources, you can research a few basic spells in the research tree, but normally you gain spells from levelling a hero, and picking an advanced casting ability (Say "Adept Firemage" or whatever its called)
Try letting go of what you remember from War of Magic, and experience FE in "new eyes"... More gamers should experience new games in "New eyes"
Sincerely
~ Kongdej