If I am understanding you there is now a battery select switch and the batteries are connect to Batt1 and Batt2 terminals and the Common is tied to the engine hot, correct?
A trickle charger is for only one battery and should not be left on all the time especially cheap ones as they will continue to provide charge all winter and the result is the battery gets overcharged and boil.
A dual bank charge is a good way to go and a bank is connected to each battery or the Batt terminal on the switch.
I recommend charging the batteries then removing the negative wire, this will prevent them from being discharged by always power things such as radio memory.
1997 2400 SCR
5.7 Vortec / Bravo 2