For charging batteries in a bank with >10amps, Battery Tender recommends the charger not be connected directly to any of the terminals. They have a good write up here:
http://www.batterytender.com/connecting-chargers
It’s to “balance the voltage drop evenly between both batteries.” Honestly I can’t wrap my head around how an extra piece of cable is different than the leads coming off the battery charger, but they’re the experts so I follow it. And yes, I do it in the rig with everything attached; with one exception, when I was bringing batteries back from the dead when the dealer drained them during warranty work, I pulled the two batteries out and charged each one individually.