Off the top of my head... here... I'm thinking a lighted LED panel mounted somewhere just to show switch status. Something easily visible that's drawn to your layout. You'd still control it with a spare remote or pad, maybe dedicated to switch control. It would just make better sense of the switch labels at a glance. That way you would be able to use the features like routes for example without much change in hardware.
I guess the problem for me is I'm not aware of a third party app that controls DCS equipment other than what I already mentioned. It sure seems like there maybe something already out there that you could remap to your layout already. I just haven't seen it myself yet.
Hopefully someone else bails me out here!