As in all partnerships, you should memorialize your agreements in writing. It doesn't need to be that complicated, you can write it in the form of an outline and both sign it.
Begin with the idea that every partnership will break up someday. You want a way to buy one another's interest out in a businesslike manner, with either of you being the buyer or the seller.
A boat survey/appraisal by a disinterested party should be the base to start from. If either is dissatisfied with one survey/appraisal, allow the opportunity for either party to have another done, and if both are dissatisfactory, a third. Specify who pays for which one. (Suggestion: partner 1 pays for the first because he wants to buy, partner 2 is dissatisfied and pays for the second. both share the cost of the third.) Somewhere there has to be agreement, no matter how unrealistic one party may be about the value. If no agreement can be made, a public auction at which either or both can bid is a possible solution, then the unrealistic partner can bid up the price if he wants to.
You want to write down your agreement on when each will use it, what condition it will be left after each trip, expense sharing, when and how upgrades will be purchased, schedules for winterizing and spring launching, how maintenance decisions will be made and paid for.
Don't allow either person to loan the boat to family and friends, sure way to disaster. But make it flexible enough so, if both agree, there can be some relaxation of this. And one agreement to do this does not mean it applies again. Each decision is separate.
Amenity upgrades need careful agreement. One partner may be able to afford his share, but the other partner cannot, due to other expenses. One way to deal with this is for each partner to contribute a small amount on a regular basis in a joint savings partnership account needing both signatures to withdraw.
There may not be agreement on the choice of amenity to buy with the "Upgrade Fund." Designate an impartial, knowledgeable boat professional you both trust who can break the tie.
Part of my work is consulting and valuing assets (not boats) for companies and partnerships that are dissolving. A good written understanding at the beginning will do away with lots of assumptions by one partner or the other, assumptions that things will be done a certain way.
You might be surprised how you both will become energized to think of things to put in the agreement, and, in the end, be happier with your relationship because you each understand. Doing away with assumptions is the best part of this, you will both be happier.