Ok lets see. You have two batteries and one is isloated right? Ok well since one battery isnt being charged it will be drained relatively fast because there is not as much coming in as going out right? So the second battery dies. But you have another battery to start the car right? So you flip the switch and can still get the car started. Thats all well and good but as soon as the stereo turns on and and starts drawing more power then the alternator can supply it starts draining the starter battery correct? So soon you have two dead batteries and no way to keep them charged.

I am not trying to argue so please tell me if I am wrong or not.

I am going off the diagram found here:
http://www.bcae1.com/battiso.htm