Woot! at least you got the lights working, I ran a separate feed to some led strips that was using a mosfet to dim the lights, if that is what you mean. If you look at the original Michael Lane thread thats what we were doing and we did just use another ground and pwm input for the moonlights, still rocking mine over my DT and works great, but you need a n level mosfet that has low voltage with the rpi.
Here is the posting that I was talking about -
https://www.reef2reef.com/threads/controlling-viparspectra-lights.698216/post-7492037
You can also look at the original reef-pi lighting controller since he does something similar, but if your wanting to dim a 12v led, you can use another pwm input mapped to do the same thing...