So ive read articles and seen maps that show morrowind as fully part of the empire, fully part of black marsh, and anywhere in between can someone please tell me exactly who morrowind belongs to. Thanks!

We can't say for sure. The http://imperial-library.info/content/skyrim-concises-account-great-war-between-empire-and-aldmeri-dominion implies that Morrowind is part of the Empire, but weakened. We don't know if the southern borders of Morrowind are the same as they were in late 3E, or if Black Marsh still holds part of it, as they did in 4E40. I assume that the latter is the case: Morrowind nominally belongs to the Empire, but is greatly weakened, and its southern borders are Argonian territory.

While Morrowind may nominally be a part of the Empire, in that Mede claims it as part of his dominion, I don't believe that the Empire actually governs Morrowind. They didn't seem to in 4E40, and dialogue in Skyrim implies that the Legion considers Morrowind as, if not a threat, then at least somewhat antagonistic. We don't really know if the Dunmer have a unified government, or have reverted to some weakened form of a Great House system with mutually antagonistic relationships, or what. It's all a bit of a mystery right now.

That legionnaire probably said that because he's so mistrustful of elves. Or the Empire in general is. Maybe the Empire is waiting for the Dominion to somehow take control of the Dunmer.