Bryan, I am a little confused, I personally see nothing wrong with two systems connected at a common point (now the purists will argue otherwise). All of this is provided you have adequate fusing.
You say a throw switch to charge either bank, is that in series with the charger output, or a means of isolating one bank or the other. To charge a bank in isolation it needs to be isolated from the other.
If you mean a throw switch to select one bank or the other at the inverter imput, not a good idea, (a) it would have to be a substantial switch (b) you would loose power while throwing the switch, most likley. A make before break switch in this situation would be highly undesirable.
Assuming I have misenterprited your post ignore all of the above.
allan down under