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does this work between 2 computers not behind the same firewall. i.e. can i sync with a computer in la while im in ny?

Yup! :)

so how is it getting around the double NAT problem? Are users acting as bridges (like Skype super nodes) or is it going though aerofs's servers?

An aerofs server is used to help establish a "connection", more or less along the lines of http://en.wikipedia.org/wiki/STUN