It can often be very beneficial to implement a state machine with a high response 'run' mode and separate isolated setup mode.
It doesn't have to be a toggle switch though. Could be a serial command. A momentary pushbutton that that toggles between 'run' and setup, or just automatically drops back into 'run' mode if there is some period of inactivity (user enters setup, but doesn't do anything for 10 second, the unit switches back to 'run' mode). It could offer a window of time on initial bootup to enter setup (say 2-5 seconds), after which it enters runmode with no option to go to setup other than resetting the unit. Different methods will be suited to different projects.