I think the stereo has a wire so you do not loose the channel memory when power is turned off - maybe that is connected to the main radio power

I did figure it out my issue. Everything was hooked up correctly except I had wired the new 6 gauge alternator wire to the batteries instead of the common on the Perko switch. After I did this everything works as planned. I did find that that it is wired to allow the tilt, blowers, bilge pump and stereo with no ignition switch.