I want to hook up dual battery's in my boat I bought the switch so that way i can run 1 battery or both.  What is the best way to hook it up?

Just remember, you asked.... 

The absolute "BEST" way to install a dual battery setup is to install a battery isolator on the charging wire coming from the alternator. One of the isolated charge wires go to the battery switch connection "1" and the other side to connection "2". then take the power lead that supplies the power to the engine and put it to common. Run the boat in "1" OR "2" and the isolator will charge both batteries anytime the engine is running.

Absolutely bullet proof and proven to work awesome. The only caution I will give you is you should have at least a 50 amp alternator. A 35 amp will work, but it wont have a very quick turnaround from a low charge to fully charged.

This is the exact isolator I have on both boats.  http://www.colehersee.com/home/item/cat/211/48120/

GT