I have recessed toggles for sidings and secondary loops so I can independently control them. I can also remotely control the transformers. Currently, all my switches and turntable whisker tracks and rotation are command controlled. I plan on having selective controls for some of the switches, but not all of them.
I use the Legacy ROUTE feature to reset things to a known state, ROUTE #1 switches all the switches to the mainline is clear. Whenever I'm switching things around, the last step can be to select ROUTE #1 and everything is aligned to run. I'm programming other routes for some more divergent routes through the layout.