If the shore power is routed through the isolation switch (off-1-2-3) then that is how the OP is isolating shore power or generator to the panel. It can't be both. I'd suspect this switch to actually an (Off-1-2-BOTH) switch.
The idea would be to wire the panel to the power post on the switch. The incoming line from shore power on one post (1), and the generator on the other post (2).
The line from the switch would then enter the panel through the main double breakers.
If you don't have an alternate power source, then you should be able to skip the switch. The switch might be nice as a service disconnect to the panel without the need to unplug the boat. OR it could be a layer of complexity and confusion that could be avoided. Your call.