Hi Noa,
With the current software, control of two state machines in a single instance of MATLAB is not officially supported - even with TrialManager.
Unofficially, if you run each state machine in a separate instance of MATLAB, it may work (you want a good, multi-core processor for this, e.g. Intel Core i7 6th-Gen or newer). Also keep in mind that the liquid calibration table uses a single file on the hard drive, so you'd have to run the separate instances with non-overlapping valve numbers for this to work (or calibrate manually).
To use this solution, run Bpod with a serial port argument in each instance of MATLAB, for instance:
Bpod('COM3') % In MATLAB instance 1, and
Bpod('COM4') % In MATLAB instance 2
Here, 'COM3' and 'COM4' are the USB serial ports of your two state machines.
I hope this helps,
-Josh