I would create and register a partnership (sort of business but you'll have to find out exactly what kind of partnership this will be as the main porpoise is not business ) which, as you mention would have to establish ownership percentage if not 50/50. Then, have the entity buy and run the boat; that way everything (expenses, maintenance and also gain/loss) will be proportional to your ownership percentage and when/if things get dissolved, then the distribution is pretty much straight forward.
I set a business like that a few years ago and my CPA helped me with the documents. You can do it on your own if you know what you're doing, or else look for an accountant or maybe even an attorney to set up the partnership.
I hope that helps.