When operating in your boat, the ACR normally always hooks one battery to the other to charge the other battery......That's is, for lack of a better word, how your battery's have been conditioned to charge all boating season long, why change that now? Still can maintain/charge them the same way with a off board charger.
The batts can be charged or maintained the same way with any charge source, the ACR doesn't care which kind of charge source it is, 3 stage trickle, engine alt, Sears automotive - 2/10/Crank, etc, etc.
If I ran a ACR, I'd just leave the "off on both" switch "off", hook a 3 stage trickle charger up to one or the other of the batts, (doesn't matter with a SI ACR type) and once the trickle charger has it's primary battery topped off, the ACR will just turn on (just like it always does with the motor running and the motor's alt as the charge source) and will automatically hook the secondary to the primary....Cept now your using a 3 stage trickle charger as the charge source, not the boat's alt.......Sounds like Dings method.
To charge/maintain them independently (best practice BTW), you'd have to turn off/disable (as Dodge said) the ACR by disconnecting the ACR's ground lead (or else the ACR will come on eventually hooking 1 to 2 or 2 to 1, see above), turn/leave the main switch to off, then hook your two bank charger/maintainer up to each battery.
FWIW, personally I don't run an ACR and have three semi permanent cheepy 1.5A 3 stage maintainers hooked to each of 3 battery's with their 120VAC plugs all plugged together in one 3 way splitter with one drop cord out the back of the boat. Back the boat in for the winter, main switches to off, plug in one cord, walk away.
