When link tracking is enabled on your account, you'll be able to set up link tracking profiles. Link tracking profiles are where you set which parameters need to be appended to your links such as utm_source, utm_medium, utm_content if you're using Google Analytics. You can also set up custom tracking.
You're then able to apply these link tracking profiles to any projects, mailings or versions you need. You can apply different tracking to certain links within an email and also exclude links that don't need tracking