Re: Battery replacement
The reason you have a switch between 2 batteries is so you can isolate one from the other. Basically, reserve one battery strictly for starting the motor, use the other when motor is off and you're running your accessories. That way you know you have a strong battery available to start 'er up. Set the switch to 'both' when the motor is running so you charge both.
One battery can't/won't charge the other. Only thing that will happen is that they'll reach 'stasis', or a similar level of (dis)charge. If one battery's charge is low and the other high, when you switch to 'both', they'll meet in the middle. If one is really, really low, you could create a situation in which neither now has enough amps to start your motor.
Conventional wisdom is that you run 2 different styles of battery- a high amp, fast-load "starting" battery, and a deep cycle type for your engine-off electrical needs. Both, however, should be of the same geneal construction - lead/acid, gel, etc... so you can use the same type of charger for both.
As far as the hybrid, combination "deep cycle/starting" battery, it's more an oversized starting battery than a true deep-cycle one. Not knocking it, but it isn't a deep-cycle battery.