I'm trying to figure out if the Avengers vs. X-Men storyline is in the current Marvel universe or a separate timeline/universe. Did Cyclops go to jail after the Avengers vs. X-Men? Are the teams "blended" now?
According to the entry from Wikipedia on Avengers vs. X-men "In the aftermath, Cyclops is placed under arrest and Captain America puts together a new team of Avengers." This is all in the current 616 Main Marvel Universe
Yes, Cyclops went to jail after the events of Avengers vs X-Men. However he was subsequently broken out by Magneto, Danger and Magik in Avengers vs X-Men - Consequences.