Not married, but long term partners and they were in a long distance relationship during Generation X. A fact that often seemed to be forgotten up to the point of Moira's death, which Sean took hard because she died when he wasn't around.
The weird thing is that despite the chemistry Scott Lobdell played with between Sean and Emma, before he left the book he had plans for a very different relationship. According to a later interview, in the long term Emma and Chamber would have become Generation X's first official couple.
Which is kinda brain breaking and was never actually hinted at during his time on the book but apparently a long term plan.