Hello Narayan,
You can run each rig in a separate instance of MATLAB. You'd start Bpod in each instance with Bpod('COM3');
replacing 'COM3' with the state machine's lowest numbered port (each state machine has two).
Unfortunately in this setup, you'd need to code around anything that uses Bpod settings or calibration, as both instances will point to the same settings and calibration files. Fixing this is on our development cue. For now, the most straightforward setup is unfortunately to use one PC per rig.
-Josh