A two battery set-up on a boat either means you have two engines with a battery each, or one engine and a domestic battery to supply all the electronics independant from the engine. The 'spare' battery is also useful if your main engine starting battery dies for some reason.
In a perfect world, you would select a standard car type starting battery for the engine and use a deep cycle leisure battery capable of deep discharge for the domestic side. Alternatively you just buy a couple of cheap Halfords batteries and get on with life
. You may need to replace them every 5 or so years though