Much thanks for the input everyone. This is my first windlass problem, and I am learning much. It seems the boat was manufactured without a windlass installed, and a PO had this one installed sometime in the early 2000s. Correct me if I am wrong, but from the input so far I understand that, if wired correctly, the windlass should be wired directly to the battery, bus or battery switch, while the control should be wired through the main panel. If the source of issue is the switches or windlass control box, the main breaker could trip while the windlass would actually still have power but no controller to operate it (hence my thinking that the windlass itself was tripping the main). I could verify whether the problem lies with the controller/switches or the windlass by disconnecting power to the windlass, operating the switches and seeing if the main still trips. Assuming it does, my solution is to then check the solenoid breaker, the control box and the switches.
If there is a windlass solenoid breaker onboard, I have never seen it. Where is it likely to be? I assume it should look like the windlass breaker?