The civil war quests revolve around taking forts right? Well what about all those other forts out there not involved in the war? I know Fort Greymoore right down the road from Whiterun gets taken by Imperial or Stormcloak forces after the battle of Whiterun if they win, but there are tons of forts out there far from the roads. If you clear these out before or after the civil war do they all get occupied? I particularly like Fort Sungard which is overrun with Forsworn. It is south of Rorikstead in the hills and is very large for a fort. So does anyone know if it will be occupied after i clear it? If so then i may make it my mission to clear all the forts

They get occupied, but not by Imperials or Stormcloaks in my experience. They just get populated with bandits or witches again.

They don't get occupied.I tried it with fort sungard and a few in-game days later,the forsworn were back

That is a downer

For me Fort Sungard got occupied by the Legion. I think it depends on the outcome of "Season Unending": Stormcloaks receive The Reach and we had to attack the fort.

What bugs me is that they aren't registered as 'cleared' even if all the bandits / necromancers are defeated.

Every fort in which I have participated in a Civil War battle has subsuquently been occupied by the victor.