As someone relatively new to this atheism stuff, I'm going to go with this:
I have no idea how time began, where the universe came from or what caused it to be.
Atheism, by definition, means 'the rejection of the belief in all gods'. This is crucial. It does not mean 'a system of belief which answers every question the universe poses'. This definition could in fact be more appropriately ascribed to many religions.
As a result, therefore, it is entirely reasonable to go for the statement 'I don't know' and that be satisfactory. Atheists would not argue 'science has a better suggestion for how time began' (we'll stick to the existence of the universe, not what happened directly after that or any other issues), but simply that the suggestion offered by religion is not plausible.
Atheism claims a need for evidence to form beliefs. Religion does one of two things:
1) Claims no need of evidence to form beliefs. For a logician, this seems ridiculous - and on that basis, that no evidence is required, surely a belief in no god is as valid as a belief in god?
2) Claims to see evidence in actions or objects found which can be ascribed to god, such as altruism or 'miracles' etc. This is one argument which can never be shot down by atheists, but will also never be believed by them as this relies on the opinion of the observer - an atheist will never see evidence of 'god's work', just as a religious person often will - it is entirely subjective.
My point is simply that atheism does not need to form theories. Completely separate from science, atheism is the concept that better theories with more reasonable evidence based logic are required to form a belief in God. Atheism, by definition therefore, does not have theories of its own. Not believing in something does not require proof. If I claimed that I was stood on a giant tortoise, it would be up to me to prove I was, not up to you to prove I’m not – it would be entirely reasonable for you not to believe me without evidence.