If I had some water buildup in the filter I would use a Mityvac or similar with a soft hose. Carefully suck it out rather than removing the filter and risk damaging it on the tank opening.I sent an email to BestRest about this as well, and here was the reply I got:
[T]he filter will collect water as advertised. When that happens two things will happen:
1. If your fuel has any ethanol additives, the water will bond to the ethanol and <slowly> pass thru the filter. That can take several days or weeks. During that time the engine will run normally and a bit of water isn't a problem. Almost all of the water will remain in the bag.
2. As for constantly removing the bag, that's not necessary. When refueling you can look down inside and see if there's accumulated water. You'd know this when your gas tank is nearly empty, but the bag shows some fluid sloshing around. That slosh is water buildup. Should this happen you can gently pull and twist the filter up and out of the tank, pour out the water and reinstall.
I've pulled my own filters half a dozen times to dump water, and as long as I do it carefully it's not an issue. Remember to use an install tool to spread the bag after it goes into the tank, otherwise the bag can remain folded and that will slow down fuel flow when you refuel the bike.