My two cents.
If I recall correctly, your original post said you were simply wanting to do routine maintenance of changing the fuel filter and you wondered if the water separator was another filter (it is not). You did not mention having had any problems. If so, why complicate things by adding another (redundant) filter and a gauge (or another pump for priming or even a fuel polishing system)?
Seems you might just follow the "kiss" principle, clean out the water separator, change the primary filter, and be happy. Of course, you can do anything you choose but, frankly, I see no particular advantage to complicating what Amel originally installed.
Cheers, Craig - SN68 Sangaris, Tropic Isle Harbor, FL