I have a 12 volt battery on a boat with a lot hooked to it ,the question is can I use a pos bus bar for the pos stuff and a negative bus bar for the negative stuffwithout doing any harminstead of having many wires hooked at the battery I'll have one pos and one negative.

Yes.

Are you using Fuses? You can have your Positive Battery Cable go to your Battery Switch, then a Fuse Block and Make all your connections there.