Take the carb apart, clear it with compressed air, check for sludge and gum and varnish and goo, reassemble it, and then follow the instructions others have given about fresh gas.
As for leaving the bowl full or empty, it is debatable how useful it is. Full, the argument is that the fuel evaporates and forms gum or varnish, and any ethanol takes up moisture from the air. Empty, the air space for collecting moisture becomes larger and you end up more likely to condense more water out of the air into the carb. Which is more damaging hasn't been conclusively proven to my satisfaction.
Your best bet is to do what you can to minimize as many of these effects as possible.
1. If you have an external tank, take it (and the hose) home with you and if possible store it somewhere that doesn't see a lot of temperature fluctuation or a lot of high temperatures. Store it with the cap on tight and the vent closed.
2. When you are tying up and stowing everything, make absolutely certain your throttle is all the way off and the choke isn't on. This will cut down on air circulation and reduce the likelihood of getting moisture in the carb bowl whether you ran it dry or not.
3. Out with the old gas, clean the tank, in with new, no ethanol gas.
4. Every now and then when you're out on the water under power, run it at full throttle a little while to help keep those jets and nozzles and galleries in the carb clean.
