Dots at 6 and 12 but rotor not in right place.

Line up the dots like normal, the slot in the drive gear has no idea how you put in the distributor. It will fit pointing towards either #1 or #6. Where you point the rotor depends on the position of the dots.

12:00 crank, 6:00 cam - point rotor towards #6
12:00 crank, 12:00 cam - point rotor towards #1