Its called a VST on the Yamahas, stands for Vapor Separation Tank.
There have been a lot of good posts here and other boating forums on how to best deal with the introduction of Ethanol fuel on boats that are already running MTBE based gasoline.
The short version is you want to do all that you can to avoid mixing the old fuel with the new fuel. It has been fairly well documented that the two don't mix well and result in a really thick sludge that will gum up your fuel/water separator and the engine's internal components.
I would highly recommend that you do what you can to get as much of the old gas out of the tank as possible before introducing any Ethanol gas. If you have to spend a couple of hours and siphon it out by hand into plastic jugs, do it, it may seem like a hassle but is better than risking major engine problems by mixing the fuels.
If you can't remove all the fuel, I would recommend that you get as much as you can, and then add as much of the Ethanol fuel in as possible in order to dilute the MTBE gas.
Since the VST tank can hold approx .3-.5L of gasoline, you can drain it out if the engine isn't going to be run for a while and you have recently mixed the MTBE and Ethanol. You basically don't want the two fuels to be sitting together in equal concentrations for very long.
If you have gone through the steps to remove as much of the old gas as possible, and add as much E-10 gas as possible and then run the boat for a while to make sure the E-10 gas has been run through the system, I don't think draining the VST tank is necessary, but it is very easy to do none-the-less, there is a obvious drain screw at the bottom of the tank.
I haven't heard it discussed much in the context of the Yamaha four strokes, but on the two stroke Yamahas there is also a filter at the bottom of the fuel pump that sits inside the VST tank. On the 2-strokes, this filter will eventually get clogged with a very fine white / grey powder, the origin of which hasn't been determined and will accumulate even if you have a 10 micron Fuel/Water separator. I have made a few posts on this topic and procedure here if you want to search on my name and the keyword VST you will probably find them.
From what I have found, there are three types of problems when switching to E-10. The first problems are caused by mixing the old and new gas and can largely be avoided if you prepare for them.
The second class of problems have to do with the fact that E-10 is a solvent and will clean out any gunk in your gas tank, and send it towards the engine. You can minimize these problems by installing a 10 micron fuel/water separator if you don't already have one. If you have an older engine/tank, keep an eye on the filter to ensure that it isn't getting clogged up with old varnish and rust and whatever else grows on the inside of a tank.
E-10 gas also has the ability to absorb more water than MTBE gas. But when it reaches the point where it can't support any more water, it will phase-separate and split into three layers.. water, weak gas and some cloudy/milky sludge. Again, this is where the Fuel/water separator is critical to prevent this gas from getting into your engine. But, if the gas in your tank gets to this point, you have a problem, and it needs to be removed or treated before running it through your engine.
Don't think a fuel/water separator is going to save you if you mix 50 gallons of MTBE and 50 gallons of E-10 gas. Nor is it going to save you if your gas tank gets contaminated and the E-10 gas absorbs so much water that it phase separates. Use the f/w separator as a way of keeping an eye on the gas that is in your tank and preventing further damage, it won't be able to 'clean' 100 gallons of bad gas.
The third class of problems are those that will come up after you have made a clean transition to E-10 fuels. I'm mainly thinking about the mystery powder that starts to accumulate on the VST filter on my engine, and I have to go in and clean it out every 100 hours to stay on top of it. I also discovered that there are other small filters inside the engine that can trap this powder and need to be monitored. On my 2-stroke, these are the Fuel Injector Filters and the Pressure Regulator Filter.
You are ahead of the game in that you know it is coming. A lot of people who had problems simply topped off their tanks in the winter with MTBE, ran their boats for a while the next spring without any problems and then un-knowingly filled up with E-10 gas and started having problems before they even knew that something in their gas was different.
FYI, I'm not a mechanic, and only know what I've read on the various forums after researching the topic on my own.
-- Tom