Here is an article by Yamaha on this subject - it is a good start:
http://yamahaoutboards.com/yamaha-a...-tips/understanding-marine-electrical-systems
What the article does not mention is that the outboard's charging system is designed to charge starting battery's but not deep cycle battery's. The deep cycle battery's will be overcharged which shortens their life. You can use this configuration & just replace the deep cycle when it fails. You could also not normally charge the deep cycles while underway unless they go dead (switch them to the crater with a manual switch), then charge them at shore using a battery charger made for deep cycles.
More complex systems from a company named Balmar are available but you are looking at least $1000 for the Balmar solution, but is is totally plug & play with no switches involved. If you are just running down riggers & fish finder probably no need for the expensive system. I have one but I have lot's of electrical powered extended trip type luxery's.