Let's go back to the original problem: dodgy fuel in
parts of the world we all love. I have always cleaned/polished the fuel from the dodgy
dock before it got anywhere near my tanks, let alone my
motor. We're not talking
power boats here, that need to take on a couple of thousand gallons; my hundred gallons (400 odd litres in my part of the world) might take me a hour to put on board instead of 15 minutes but I know it's clean because it's gone into my 5 gallon plastic tin that is continuously pumped through a couple of filters (50 and 10) before it goes into the tank. A hose from your polishing system up to the
cockpit with a hose fitting into the bottom of a plastic 5 gallon tin is all you need.
After that Kenomac has it completely correct: leave the tank absolutely full when you
winter over. All of the nasty stuff forms on the surface of your fuel where air meets
condensation and fuel. If there is no space for air and
condensation then no "bug" forms.(One of the reasons you get bad fuel from poor places, they never fill their supply tanks.) So polishing fuel that you put back into the same tank misses most of the problem which is on the surface (not the bottom) of the tank.
For about 20 years, I only had a few hours a week to go
boating so I bought a 50ft stink pot with two 3 hundred gallon tanks. At least twice a year I'd take the stink pot for a hard bouncy ride and then run one tank dry through my polisher into the other tank. The initial stirred up bottom would produce a bit of stuff, but 90% of the crap came from the last gallon on the surface of the tank.
Xlantic has it right as well; a day tank is the best. Every super-yacht in the world has one for just this reason. A day tank has the return to the main tanks at the top, so the surface "bug" problem never forms (it's full every day), and the feed to the motors at the very bottom, so that there is never any crap in the tank; the polisher feeds the day tank until it over flows back to the main tanks. You then just need a basic filter and
water separator after the day tank.
DeepFrz and Kenomac both have it completely right regarding leaving your polisher on a timer when you're not there. I'd never get to sleep thinking about fuel moving around my
boat when I'm not there. Just fill the tank right up (through your polisher) and it will be fine when you come back.
As an aside, my wife tells me we're moving to the dark side and
buying a
catamaran so she can cook and talk to me at the same time! When we do (the male on this
boat is not necessarily the captain) I will immediately install two small day tanks (say three gallons each) fed from my polisher. I find it almost unbelievable that all production catamarans run one
fuel tank. (Please tell me I'm wrong!) The greatest advantage of two motors is if one dies you have the other. But, the most common reason for running diesels to stop, is fuel quality or lack thereof, so one tank supply to two motors is crazy.
Yes, the water-diesel interface is also a good "bug" breeding space. So make sure your
diesel outlet is at the very bottom of the tank. Some
boats have it a half inch above the bottom, I'm sure that that is to insure that the
builder gets a few years and out of warranty before the sludge gets to the input!