Gonzo, others may (will) have a different opinion on fuel polishing, but mine is that if the diesel can sit for a year plus, you'll wish you had the ability to polish it at some point.* I prefer a system that moves as much fuel as possible, since when underway, polishing the fuel means removing the crud that precipitates out of diesel as it sloshes around.* Slow flow systems don't do as good a job as those moving more fuel, so something like the Racor FPM doesn't really appeal to me both from a cost and functionality perspective.*
So, those are my biases, and based on that I'd say because your tanks aren't that large you are marginal on the need to polish, but because the fuel may sit there for awhile and you can afford to put in a system and there is room for it I'd say go for it.* There is no downside other than cost that I can think of.*
The system I would put on your boat would have the supply and return manifolds made out of 1/2" JIC fittings.* Since you only have 2 tanks I don't see the need to make up or fabricate separate manifolds.* If you think you would add a day tank later, include an additional capped port.* I prefer 120 vac motors where to voltage is available because they are quiet and last a long time, and the carbonator style mount (48YZ mount) is super easy to set up to a ProCon vane pump that you can buy to match the filter you use.* In your case, a Racor 500 will pass 60 gph, which should be plenty so the ProCon pump would be a Grainger part number 6XE80, mated to a 1/4 hp motor, Grainger part number 5XB85.* This motor pump will cost you less than $200.00.* Since 60 gph is all you need, the Walbro pumps could also be a good choice, although I think Phil said they were going to stop making them.* Make sure you use JIC fittings unless you like leaks, and you can get what you need in this department from any hydraulic hose shop.* A timer is nice so you can turn the unit on to polish for a set period of time, and you can find one at Grainger as well.* When underway and the inspiration hits you, polish away.* I run my system 50% of the time and after 4,000 gallons or so have changed filters 4 times, but never drained a teaspoon of water out of the Racor 1000s.
Just my two (three?) cents worth, although I am sure others will have a different approach.