I would say it depends on how you want your power running relative to the switch on the dual batteries. Is one battery for starting and the other for running the stereo? Or or you having dual batteries for backup purposes? The amp power will still need to be hooked up to the positive on the battery, but you might need to run a split to both if you want to have music regardless of what battery you are using.

A perko switch will only allow one to run at a time, like a gas tank selector switch. From what I know most guys run dual bats and a perko. They run and listen to the stereo off of one battery while the boat is running and when it is off. The other battery is a back up to start it and then you can switch back to re charge the first. Or variations of that like using the second battery for stereo on when the boat it off. The voltage would only double if the batteries were wired in series, don't do that lol.

Anytime

I have two batteries. One for starting/running the engine and a deep cycle for radio only. My stereo runs on #1 #2 or both batteries. But i only use the radio on the deepcycle (#2) battery when i am beached or floating. I have nwver had a starting issue. I have never had to use Both to start because the #1 is always charged. If you have a large system then maybe use two batteries on the number 2 side. But my single deep cycle has lasted all day running my 10" sub and amp without dying on me.

how bout them trojans bra.. now thats out the way i run a locking perko(has its own key) and hide it cuz im bout thieves n i use one batt just for start and one for electronics u can always just pull n swap batts if motor batt dies here are some diagrams that maybe will help