My machine is a lathe with a milling head, run off the same motor. I have no pulleys on the lathe drive - that is more or less direct. There are a couple of pulleys on the mill head, but I have only bothered with one yet.
The way the automatic configuration seems to work is that the computer puts out a PWM signal to your driver board, starting at a low speed and ramping up, and then compares the speed it thinks it has set with the actual speed as per your spindle inde. Mine spindle seemed to be about 10% too fast. I would have thought then you would do it again and the computer would gradually adjust itself until it was correct, and announce itself.
It doesn't seem to matter how many times you calibrate, it always goes through the same procedure, but when you save, shut down and then restart the speed setting appears spot on (It is on mine anyway)