Standard practice is all bonds are one system and all DC grounds are another. They would tie together at only ONE point, which if you don't have a dedicated grounding terminal is usually the engine. If you don't ground the engine to the system you will have a DC current path through the water and not be using the zinc to protect the rest. (btw, here is my ground point:
http://www.bluesea.com/products/cate...tors/PowerPost)
Also - if you are using this as a lightning ground with shrouds and mast connected, you don't want the engine to be the exit point for lightning! I would tie the mast and shrouds together at a keel bolt or other good lightning ground and branch other bonding out from there.