Like I said I love
this idea, but the real issue of creating such a place is that there is no binding doctrine for being an atheist. monotheistic religions have a binding supernatural delusion, usually with a specific text and shared culture, this is what gives them cohesion. It allows the 'headquarters' to exist because they all share the belief that this particular group is 'in charge' and even with that religious people who follow the same text fight about who's in charge (as a protestant about the Pope).
So I'd say the atheist temples
of science and natural history, technology expositions and their churches
where people are educated and proselytized too are Universities
So rather than a headquarters are we not looking for a focal point? Not so much a headquarters as a Mecca
place that all atheists whether physicists, chemists, biologists, astronomers, social commentators or any denomination of atheist, humanist, transhumanists etc. would be motivated and compelled to visit in their lifetime. No matter the distance, almost like an atheistic pilgrimage .
It could offer a wealth of knowledge of all the sciences, an extensive library, rooms for debating and education on subjects, curators and professors who create creative commons educational material for the people of the world, and of course conventions and speakers with organisations like the AAI or RDF. Certainly this is no mere building it would be a vibrant and active place, what we need to do now is define what
we're creating it for and how
it would work.