Mike:
I'm with you on getting the controls off the layout surface. I used a simple pine shelf to hold my controls along with a hinged control panel supported by two pieces of pine, all painted a neutral color (left over from another home project).
Running TMCC, I elected to use switch controllers only for frequently used switches and run the rest through TMCC.
Your efforts are inspiring and I covet that beautiful Super "0" track. Keep up the good work!