I just talked with my mechanic about this as well and he echoed what Rip Ryder said. Run down your tank until near empty before refueling with the ethanol fuel. New and old do not mix well. Keep an extra water seperator filter on board. You'll know when it is time to use it. It doesnt actually sound like any particles or sludge would actually make it through the water seperator filter (we hope). I have been using an alchohol based additive for a number of years , Evinrude 2+4(which has really helped the performance of the engine) but you do NOT want to use these with the new fuel. However, Yamaha owners can continue to use Ring Free. They also said not to leave the ethanol fuel dormant for 60-90days(not a problem for most fishermen). Which means next winter we will probably be storing our tanks empty. They also said, a little too seriously, to cross my fingers.
I would really like to hear from NY boaters that have already gone through this if you have any advice or warning signs to look for; especially with fuel line issues as mine are going on ten years this summer. Thanks in advance.