One bank (in your case, with both batteries combined) is always simplest. Of course, you do run the risk of accidentally draining the battery with accessories. The alternator should not drain the battery when it's not running, if everything is working properly. Just like a car. That happens to be the setup we have on our boat. We sized the bank so that it's big enough that we don't deplete it. That would be impractical on a larger vessel.
Since you already have the battery switch, you could leave it setup as now. Just run the aux on "both" -- and when not motoring, switch to whichever bank you want to call "house". The next time you're going to fire up the aux, again switch to "both" (first) and everything should be OK. You could even alternate which battery you call "house", say, batt 1 on odd-numbered days, and batt 2 on even-numbered days. Since your switch isn't the make-before-break type with a field connection, just remember to never move the switch while the alternator is running.
A shore-fed inverter/charger shouldn't be an issue. They are typically setup to handle 2 banks for charging, so you can feed to each bank, and the switch position during a shore charge would be irrelevant, as long as the charger allows combed outputs. Ours does. We have a Guest 2-bank charger, but combine both outputs into one bank. Works "swimmingly", as the British might say.
The better chargers on the market now, and I think Xantrex is one, can proportionally charge whichever battery needs all the amps. In other words, say you have a 2-bank "nominal 10 plus 10 amp" charger, wired to 2 banks, and one bank is already topped up, these kinds of chargers can direct the full amperage (in this case, 20 amps) into the bank that needs it. Very nice.
As mentioned, if your inverter needs are only for an occasional cell phone charge, you could just use a "pocket" inverter plugged into a "cigar lighter" power outlet, up to about 75 watts or so. However, a sophisticated inverter/charger is a great convenience, since the AC outlets can be live even when the shore power is disconnected.
Paul Van Voorhees
Certified Tohatsu TLDI Technician
Mgr, Obersheimer Sails
Buffalo, NY USA