Some controllers require you to disconnect from both the panels and battery bank (in that order) to make changes to settings. Then connect back up to bank, then panels, in that order.
It's no different than hooking up a portable charger... hook up clamps first, then plug in to 120v.... when finished, unplug from 120v, then remove clamps.
controller to battery:
If controller and batteries are far apart, or difficult to access, install a fuse or cb near batteries to protect wiring, and an on/off switch near controller to disconnect/reconnect circuit.
If controller and bank are close to each other, and easily accessible, install a switchable cb near batteries to both protect the wiring and disconnect/reconnect circuit.
panels to controller:
install a fuse or cb near panels to protect wiring, and an on/off switch near controller to disconnect/reconnect circuit.
fuses/cb's sized to protect wiring... so higher than controller's input and output, but lower than what the wiring can handle without getting hot.