They way you purchase a used boat sold by its owner depends on how you find the boat. If you are using a classifieds site, such as Craigslist.org, iBoats.com or ISoldMyBoat.com, you need to contact the seller directly to work out payment. Auction sites, such as eBay.com, handle payment.
Classifieds websites function in a similar fashion to the ways traditional paper classifieds work in that they simply allow users to post ads for other individuals to view. As such, classified site owners don't usually involve themselves in the actual process of purchasing the boat. For example, Craigslist allows a seller to include various contact methods, such as an email address or phone number, in ads so that a potential buyer can reach out to him directly to discuss the actual sale. In this scenario, you would pay the seller in his preferred method and most likely retrieve the boat yourself.
Alternately, eBay.com takes a direct role in all sales conducted on the site. Boats are sold either through an auction, wherein you purchase the boat if you have the highest bid on it, or a direct sale which allows you to pay one price and immediately buy the boat. In both cases payment is processed by eBay and delivered to the seller.