You got it right. At 6-12 the rotor should be pointing at #6, at 12-12 the rotor should be pointing at #1. You can put it back together either way.
If you put it back with cam/crank in 6-12 position and rotor at #6, when you rotate 180 degrees it will be at 12-12 and rotor at #1. And vice-a-versa.
If it is a new cam, you ought to degree it to confirm the valve timing.