Starting batteries (cranking) are designed to discharge a large amount of energy for a short period, which is why these batteries are ideal for starting engines. Deep cycle batteries are designed to discharge a small amount of energy over a long period. It's a matter of choice of which and how many accessory loads you tie to a battery. Be that as it may, I choose to use what I'll call logic when deciding which accessory to tie to which battery. I personally do not load any accessory to my cranking battery. If you were to tie an accessory that you use with the engine off (stereo, depth finder, etc.) and you use too much "juice" while the engine is off, you won't have enough juice to start the engine.
In essence, if you have battery powered accessories on your vessel then 2 batteries should be the minimum number of batteries you keep on board...1 cranking battery and 1 deep cycle battery. How about if you have a 24v trolling motor on your vessel...this would indicate the need of 3 batteries...1 crank and 2 deep cycle.