If your encoder has three simulated 'Hall' tracks, I have done it with a double beam scope, as follows.
Connect a 10k ¼w resistor to each phase and connect the other three ends together to make a star point. This is you scope common for the first channel and the input lead to the U phase.
the other 'scope channel is for the hall effect output for the U pulse.
Rotate the motor either by hand or by some low speed means and a generated sine wave should be observed on the U phase out. The square hall effect pulse should be then aligned with the the centre of the sinewave output.
The other Hall pulses can be verified the same way with the corresponding motor phase.