Ok i wasnt sure if the title was good, but i have a quiestion. I noticed you are taking over forts for the empire if you are helping them, but can forts that arent affiliated with those quest be taken to? or places with a fort mark and a flag?

PEACE

You can only take over the Stormcloak (or Imperial if you affiliate with the rebellion) forts involved in the quests.
All the other forts (except some quest-related ruins) belong either to your faction or bandits/Forsworn. You can clear out bandit forts, sometimes as a bounty quest for a Jarl's steward.

Ok... just finished imperial now, so Skyrim is as fully under imperial control as it can be.