This is probably the most widely discussed and disputed topic when it comes to winterization. Variations in regional climate compound the discussion. I look at this like an old school/new school debate though at this point I think it is so old even that doesn't apply. I can tell you this, despite what Mercruiser says, I leave it full. There are up and down sides to either. Leaving the tank empty significantly reduces phase seperation (fuel going old), however it causes a condition where condensation builds on the inside of the tank walls and then 'rains' into the tank. You can potentially end up with water at the bottom of the empty tank.
Take a look at what Mercruiser officially says:
What should be done when storing boats with ethanol-blended fuels for extended periods?
Follow the instructions for normal storage preparation found in the Operation, Maintenance & Warranty manual. When preparing to store a boat for extended periods of two months or more, it is best to completely remove all fuel from the tank. If it is difficult or not possible to remove the fuel, maintaining a full tank of fuel with a fuel stabilizer added to provide fuel stability and corrosion protection is recommended. It is best to add the stabilizer and fuel treatment to the tank at the recommended dosage, run the engine for 10 minutes to allow the system to be cleaned, shut off the fuel valve to interrupt the fuel supply and allow the engine to run until it stops, and top off the tank until it’s full to reduce the amount of exchange with the air that might bring in condensation. Do not cap the tank vent and do not fill with fuel to the point of overflowing. Some extra space should be maintained in the tank to allow for expansion and contraction of the fuel with temperature changes. A partially full tank is not recommended because the void space above the fuel allows air movement that can bring in water through condensation as the air temperature moves up and down. This condensation could potentially become a problem.
Mercury Marine Fuel System Treatment & Stabilizer can help maintain fuel systems in storage. It contains oxidation inhibitors to reduce oxidation and gum formation, metal-chelating agents to protect metal components from corrosion, water-absorbing agents to reduce the presence of free water, and dispersants to help suspend and disperse debris. When placing the boat back in service, be sure to reopen the fuel valve to the engine.
Note that while they do recommend leaving it empty, they also acknowledge that it CAN be left full as well. My opinion (Hey, I'm just another guy with a computer, internet connection and opinion on the internet) is to leave it FULL and do the following:
1) Add Stabilizer designed for maring environment and ethenol:
2) I also put in some Stay and Store as well (1 of the following):
3) Startron: This will handle any water which does develop in the tank during storage
It is ok to put in all three. Then top off the tank. Running it long enough to push ful through the pump and engine is a good idea. Your going to put the outdrive on muffs to flush the engine anyway.
Don't forget to drain the engine.