Your doing the right thing, run the gas out. If you leave gas/oil/ethanol in carbs for a few months your best case scenario will be a very hard engine to start at the boat launch and maybe a dead battery.
If you do run a boat that's been sitting up with do this before you try starting
1#Disconnect Hose then purge line with fresh gas
2#Connect fuel line prime bulb
3#Drain carb
4#Re-Install Carb screw plug
5# Repeat steps 2,3.
6# Prime bulb, choke and start
Carb jets don't like oil and water.
Spark plugs don't like to ignite oil and water, especially when there cold. Give your plugs and engine the best chance to start from the beginning. If you get real desperate and it's cold outside, throw your spark plugs in a toaster oven.