The solar controller is powered by your batteries, not your solar panels so you don't want to disconnect the controller from the battery bank to shut down you solar system as the controller will need to reboot and reset each time it is powered up. Rather, the proper way to turn off or shut down your solar system is by opening the positive wire from your solar array to your controller. We suggest a simple on/off switch in the positive wire from the solar array to the controller. Turning the solar array on and off with this switch will do no damage to the solar system.
There is a reason it is desirable to be able to shut down the solar system with the switch or breaker between the solar panel and the controller. When charging off the alternator, you want maximum output going to the battery bank for bulk charging until the batteries are up to proper voltage. Some alternators, especially alternators with smart regulators sense the state of charge of the battery bank and determine to apply either a bulk or a float charge. If the panels are connected and producing, the regulator of the alternator will see the sum of the battery charge plus the solar charge coming from the panels. This apparent heightened state of charge may result in the regulator putting the alternator in float mode prematurely because it thinks the battery bank state of charge is higher than it really is. The same applies for the shore charger. This condition only occurs with certain combinations of alternator regulators, solar controllers and shore power chargers. Most of the time it is not an issue. Confused? As a general rule, to be certain of getting the maximum performance from your engine alternator and your shore charger, open the solar breaker when they are in use. Otherwise, experiment with your equipment and see if there is interference between the units as described above. If not, leave the solar system on all the time; that is what we do.