With the fall update in 2007 microsoft included the ability to change the windows live id associated with a gamertag, but you can only do this once a month. So if you are having trouble linking an account to bungie.net, just create a new email and change your email through your account management on the gamercard, problem solved.
Your account settings which is everything that shows who owns the account can be edited in both the gamertags account management and the account management on xbox.com, either works.
Post questions if you need to know any more.