Glad I could help!
You actually don't need the other folders in the path Unfortunately, the Gen2 Interface is still undocumented. You would start it by creating a Pulse Pal object in your workspace:
P = PulsePalObject('COM3')
Then, edit the fields of P to update simulation parameters, e.g:
P.phase1Voltage(3) = 5.8;
P.restingVoltage = [2 2 5 -5];
The functions of the old API are called as methods of the object:
P.sendCustomPulseTrain(TrainID, Times, Voltages)
or
P.trigger(channels)
To see a list of possible functions, type
methods(p)
We are working on the GUI, and the new API will be documented once the UI is ready.
I hope this helps!