I have been playing with both modes and set it on the mode that gives extra effect to the front wheel. When I stop, I use a little front while stepping on the rear to point where I feel the abs kick in. That's when I give it more front.
Not just complicated, I don't really know what you mean. You shouldn't feel the ABS kick in unless you have stomped on the brake enough to have the sensors believe a locked condition is imminent and takes over modulation of the braking to prevent the wheel from locking up. I think what you are feeling is the pulsing of the linked calipers. I use both the front and rear brakes as I would any bike, which is to say mostly front but with definite input on the rear.
The owners manual states in more than one place that the rider should use both brakes as you would a conventional system. They engineered and built the system, there must be a reason they recommend that procedure. For me, it's so my muscle memory stays fresh, in the event I'm on a different bike or the ABS craps the bed on my Connie, and because I like to feel that I'm involved in the total procedure of proper riding.