You can use the stabilizer IAW instructions for every fill up. However, I would consider using Valvtec which has both a fuel stabilizer and a decarbonizing cleaner. Here where I am, on the Chesapeake, several of the marinas sell gas pre-blended with Valvtec, which is actually cheaper than buying it retail and adding it yourself.
I assume you are using a fixed tank in your boat. If you are, then you probably need to drain out the remaining gas, and start with fresh. Here is the procedure I've used to drain a boat tank. I'm sure there are other methods that work just as well, if not better.
I purchased an aftermarket 12V electric fuel pump from an automotive parts store and rig up a plastic hose on the intake side that will reach to the far corners of the tank. I remove the plate that has the fuel pick-up hose connected to it. (Be sure to clean the screen on the end of the pick-up.) Then I raise the bow of the boat and tilt it slightly to one side so the fuel will accumulate in one corner of the tank and pump the fuel out through a standard, clear, inline fuel filter rigged up to the outflow side of the fuel pump. That filter will show you how much crap you are getting out. You will likely need to clean it out often. Also, pump the first several quarts of fuel into a clear glass container to see if there is much water and junk are in the bottom of the tank. You can use the remaining fuel (less the water) in your car or truck. Then put in a couple of gallons of new fresh fuel, drop the bow and slosh it around in the tank as best you can to pick up remaining debris. Raise the bow again, and pump that out, using the same procedure. That will get almost all the crap out of the tank and the external Racor fuel-water seperator will take care of the rest.
By the way, that electric fuel filter can be used for many other tasks around the home, like draining lawn equipment tanks, and transferring other fuels. It's relatively slow, but works consistently and safely.