I've just written a simple sketch that toggles the program between two modes which I've called "automatic" and "manual" on the repeated push of a button. In each mode, there's an empty function (well, it has a serial print to prove it got there) where the "real" code for the respective modes would be added.
It also holds the sketch at the bottom of setup() with a while(), which await the press of a button.
Idea is that setup() could run some kind of calibration and then await the operator's say-so to move into loop() where the process is run in either automatic or manual mode, with the operator able to switch between those modes.
I'll post it soon in a new thread... just need to comment it 8) and do a state diagram. I'll explain it in the thread where I post it.