WordPress MU Affiliate without using Affiliate URL

Hello,
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.
Joseph