What's wrong with saying 'I don't know?' Demanding that atheists know how the Universe came to be seems just as wrong as demanding that you explain how God came to be. Except that the atheists can at least claim to have at least some evidence that the Universe exists (even if it could all be false), so they can at least start their search for an answer with relatively solid footing.
If you are in a normal discussion as to how something knowable works but of which you have no knowledge, saying "I don't know," would be quite reasonable. Unfortunately, quite a few of the "true believers" seem to take someone saying, "I don't know," in this context as an invitation to be "educated" with their particular mystical explanation. So, unless you want to hear the current mystical explanation, just say the scientific explanation works well enough for you and let them expend their energies attacking that. It's usually much more entertaining than the lesson you get with "I don't know."
Maybe, "I'm OK with not knowing," would work better than "I don't know." Trying to convey that you're more comfortable with a blank slate than one that is filled with mystical gobbledy-gook is hard to get across to those who embrace the mystical gobbledy-gook.