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Hines,
The battery switch should be located near the battery(s) whether in the console or near the transom.
The fuel water separator should be mounted on the transom out of the way. The transom has wood where the sides of the boat or the splashwell is only fiberglass.
Yes, somewhere out of the way in those locations. Your hoses and wiring should already be in place I assume, so without seeing any photos, choose a good spot.

I did not have a fuel/water separator on my Montauk because it had portable tanks.
My batteries were located in the console so that is where I had the battery switch.