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

It's fine as far as the gears go. just take the motor and get everything else set up like valvetrain, balancer, etc. then last before you put the intake on crank the motor over till you feel compression on number 1, then just line up the balancer to the timing mark about where you want you initial to be. now like crackedback said just put the drive gear in where it lines the distributor on to fire #1. remenber the crank is 2 turns to 1 cam turn so you are timed just at a different point of the 360 degrees of rotation.