In BTS software suite, that it is supposed to be very similar to Vicon's, you can modify the provided biomechanical template to add your two custom additional markers.

I think this could be a valuable resource: http://psy.mq.edu.au/me2/mocap_v1/subject_prep.html

You could alter the template through the way Matteo suggested. But if you are not too familiar with the software, the easy thing to do is by assigning upper limb marker labels to the two new markers, since you aren't analysing upper limb anyway you could ignore the upper limb markers. But be careful when you use the software to calculate joint angles etc. 

Thank you for your answers.