There are 4 breather tubes on the carb. 2 are oriented up so take those 2 and run them up into the airbox. You can take it a step further and put the ends of the tubes into a film canister and pack some air filter foam into the end to keep dust and debris out.
there is also a hole (for brake light wiring) from the airbox to the rear fender. have had a lot of water go through there before i realised that it was there, it is now duct taped
You can put a piece foam in there to block the splashing, but still allow some draining.
There is a company that sells one way check valves for the lower vent hoses.
well, you'll never make a submarine out of it, but see some of the other comments. First and foremost, if the carb can't breath it can't pump fuel into the motor.