Did you become atheist first, or meet your partner first?
For me I was in a relationship w/ my Catholic husband, I was in my pagan experiment at the time (being that he was fine with paganism and even went to pagan festivals, he's a pretty open-minded Catholic). I became atheist over a year ago.
He accepts me even though I don't think he really "gets" it, and he sort of thinks I keep changing my religion. Before my pagan experiment I had spent my childhood going to UU church and celebrating a few Jewish holidays if we remembered to.
I accept him even though I also like to debate. Sometimes he's gotten defensive and then I've told him if it makes him happy to believe that God answers his prayers, etc, then I want him to be that way and I support him fully. I certainly don't want him to just go along with whatever I say! And since I have been the one to change my views over the years, that would be a silly thing to expect.