It seems we've had this discussion before in another thread...
I too have had the interaction between solar panels and alternator, which resulted in the cycling on/off of the alternator every few seconds. Very annoying. So I shut off the panels with a switch located between the panels and the solar regulator. I agree with the earlier comments that the breaker or fuse needs to be just before the battery, while the switch is probably better placed between the solar panels and controller.
All of my charging sources (alternator, wind vane
, solar panels - except the battery charger) are connected to the batteries through isolator diodes. Besides assuring that all batteries get charged, it prevents shorts in the wiring
or charge devices from dumping the power from the batteries and starting a fire. Recently I bought a dual output Morningstar solar regulator so I will be using fuses
instead of the diodes for solar. I already have fuses
on the wind generator
(in addition to the diodes) and battery charger