Just rip it like an other movie. Then name it in a way that makes sense to you. If the bonus disc has one feature on it, this is easy. If the bonus disc has 4,5,6 or more features on it, this becomes more difficult to manage.
Some people have devised ways of using extra fields to help categorize this type of thing. I started doing that, but never got very far. I may revisit my "bonus features organization" method at some point.
Brian.