You need to align the phototransistor pulse on the 6th stable position of the motor and also align the clock platter to the 12h00 position.

The PC application is here to help you!

• tick the checkbox  

• the disk will lock on the calibration position.
• unscrew the platter
• rotate the bottom disk until the led switches on
• rotate the top platter until it shows "12:00"
• screw again the platter fixations

As it is not totally easy to understand, have a look  at this video 

Your disk is now ready to run. Anytime the led flases, a full rotation is finished!