Man this is a great question and topic.. I am an insurance adjuster that works boat claims and I can tell you that it is very important to have your lights on correctly. A good rule of thumb is, if you see green, You have the right of way, if you see red, they have the right of way..
The basic maritime rules are in the back of the fishing and hunting guide that you pick up at Wal-mart.
I can also tell you that if anyone is so unfortunate to be involved in a boating accident at night, that the liability will be based heavily on proper boating procedures regarding running lights. I have worked claims where boaters have run aground because some one didn't have the correct lighting or were using lights when not underway.
My suggestion would be to make sure that you are very aware of the rules of the water.. Laws are very different on the water vs the roadway. If you don't know the correct passing or overtaking laws and there is an accident you may very well be at fault even if someone turned into you, or avoided you because they thought you were underway. Be careful out there!!