You should be able to download the wiring diagram from Winnebago.
But as far as I know, most Solar controllers are directly hooked up to the battery from the solar panels. The only way to shut it off is disconnect the solar panels. But I would not do that. The whole purpose of having solar is to maintain the batteries, even during the storage period. The Chassis disconnect switch shuts off output from the batteries NOT input.
Just let it be that is what it is designed to do, charge the batteries.