[JRTJH]

Yep, The charger should be connected to the POS terminal on one of the two batteries and the NEG terminal on the other battery, as shown in this diagram. Connecting the POS and NEG to the same battery, whether it's the battery on the left or the battery on the right, will charge the battery the charger is connected to (the PRIMARY battery) and will only provide a "slight parasitic charge" to the other battery.

To fully charge both batteries, the charger should be connected as shown in the diagram. That way both batteries are "in the charging circuit"...