Let me start over.

There are no switches in the boat at all. All it had was 1 very small battery and it was running everything in the boat. I added a system and some other things in it so I know it would need 2 batteries.

I have 2 big batteries and a 2 bank for it, right now everything is just sitting in the floor of the boat. I didnt buy a switch because I was thinking about my bass boat electrical system and thought it would work the same. I dont know if it will or not thats why I was asking. This is my first ski boat so I am still learning how it works.

If you're using an ACR/VSR then the scheme will definitely change according to the particular brand. And in most cases you'll have to add a supplemental switch for isolation during AC charging. A bass boat is a little different because the outboard motor has a very small alternator or stator comparatively, which cannot charge a depleted bank with a considerable amp/hour capacity. So the trolling motor bank remains in total isolation from the boat's electrical/charging system and is completely dependent on AC shore charging for restoration.
I assume that since there was only 1 battery in it from the factory it would not have an ACR/VSR. I understand the Perko or whatever so I could use both in case the system kills the boat. But I was thinking about both batteries being totally seperate from each other.
#1 for the boat
#2 for the system and power inverter

#1 would be just like it came from the factory and charge from the alt.
#2 of course would need to be charged by the 2 bank alone.

The 2 bank would be hooked to both batteries and charged when I get home.

Does this make any sense at all? It does to me as I am typing it, but I know reading it and typing it are not the same. Maybe I need to put the crack pipe down for a little bit.