WordPress MU Affiliate without using Affiliate URL

We have the admin bar enabled at the top of all of our sites. For users that are not logged in they see a link to signup for a free blog.
Question: When a user lands on one of our network sites at a different domain then our main signup domain, Does the affiliate code check check for the existence of the cookie and create a new affiliate cookie if it does not exist. And then from there if they do not actually click on a referral link just click on the signup at the registration bar does it track that through some how?

I guess I am trying to wrap my head around how it works.
Thank you for your time.