Hope this helps someone in the future looking for this information.
There are two methods to hook up the Skene controller and any aux light onto a GL1800. I'll briefly explain why I did what I did.
Method 1: Exactly as described in the literature provided with the controller. In this manner, you'll always have aux lights as well as hi-beam lights with a single flick of the switch. Living in the great southwest, there's times that in certain locations (oh, let's say your neighborhood...) you'd want a bit of extra light (hi-beams), but NOT all of the light you have on the bike. I'll leave it up to the reader to ascertain if this situation, or others that you may experience, be the reason you're doing this. If you need a bit more choice, you should use Method 2 below.
Method 2: Simply add an appropriate-sized relay to the output of the Skene controller, and have the switch that controls the relay an independent switch. In my case, I can do low-beams and high-beams, just like OEM. The way mine is wired, with the low-beam active, hitting the aux light switch, the aux lights will illuminate at the 'low' setting (20%), thus they can be used as a kind of driving light. When I hit the high-beam switch, and the aux lights are off, again, normal high-beam illumination. With high beams active, the aux light switch energizes the Skene, which provides 100% illumination. The Skene controller needs a signal from the OEM wiring on the status of the lo/hi beam switch. This is tapped off the OEM control line that would operate the OEM driving lights. This is the 20%/100% function of the Skene without having to mess about with any other switches.
Wiring of method 2 is a bit more complex, but if you're taking the time to do this, might as well have as much flexability in how the lights function.
For me, this is the best compromise out there.