Andrew I haven't owned a Yam 50, but on other Yamahas the earth (black) normally goes to the start motor chassis and the positive (red) goes to a soleniod connection. Your right, you don't want to get this wrong so have a dealer show you. Also consider a battery isolation switch in the positive battery cable and if your going to fit electronics then a second circuit with fuses or breakers would be sensible. Rogue Wave and I like the Blue Sea stuff so worth having a wonder around a decent chandlers.
I asked Jon Fuller how he recomends batteries be secured in a powerboat a couple of years ago and he came up with this photo of his installation
which looks good and way better than a plastic battery box, so in the best traditions of Ribnet, I have splashed his idea and had a local firm make up the 2 frames to secure a battery.