Hi,
If you have both ug degrees then you have a choice as to which Mark's should be considered for shortlisting. While filling your CAT form just fill the Mark's of the degree which you want them to consider.
After you have appeared for CAT you get shortlisted for different iim's  and they will send their own form and in this form fill the Mark's of both the degrees . The details you will fill will not be used for shortlisting , it will be used to make your profile which will used at the time of interviews.
Hope it helps...