To register your tracking domain, go to your account and enter your domain name there. You must prove ownership of the domain and they do this in a similar way to the way Google does it for google apps; either upload a file to your web root, add a verification code into the header of your homepage, or change your DNS settings. I added the verification code to my wordpress template simply because it seemed like the fastest way to get the domain verified and tracked.
I find it really interesting to see which pages on this site get shortened and shared - it really encourages me to keep on writing and sharing here, even when things are busy. Looking forward to seeing what bit.ly's stats will show (I set this up about ten minutes ago, so there isn't much to see yet!) - if you're using this already, what do you find it useful for? Leave me a comment!