there are basically two types of marine stereos.
type one is a portable stereo, powered with a bunch of normal C or D batteries, or plugged into a cigarette lighter.
type two is a permanently installed stereo, like in your car, but able to withstand the marine enviroment.
it connects to your 12 volt starting battery, or to a deep cycle used for trolling if its only battery you have.
powering a stereo with a deep cycle just to be using a deep cycle is pointless with a basic stereo and its low power consumption. start adding subwoofers and amps, and try listening to music with the motor and its charging system off, deep cycle is the ONLY way to go.