Yes, always bench bleed.

If yo don't get all the air out on the bench, it will become very obvious while bleeding the servos, as you wont achieve a high, hard pedal.

A tip if you find yourself in this position: you can get the remaining air out of the master as thus:

With the system full, and most air removed, press the pedal slowly to the floor. Release quickly. Repeat. The remaining air will bubble out of the master through the reservoir.