Gary,
I have a nominal 150W of solar panels ( though I never see that much output in practice) and two Trojan T105 6v batteries in series (very good, and about 200AH), with a 20A controller and fuse linking them. That charging circuit doesn't go through the battery isolating switch, it is "always on".
Quite separately, the alternator, and the output from the battery to the 600W inverter and to the power distribution board (15A circuit breakers) are connected to the battery through the isolating switch.
The windlass, the major power user, is connected to the isolating switch via a 135A circuit breaker.
Thus, there is no interaction between the solar controller and the rest of the system, and the controller only needs to be sized for the amount of panels you have.