You would have to isolate the batteries with a switch in the pos. parallel cable. The pos to the meter would connect to the 3rd post. You could monitor 1,2, or both (as one battery).
So, pos of batt 1 to switch post #1, pos of batt 2 to switch post #2, meter pos to output post (com) To monitor batt1, turn switch to #1, to monitor batt2, turn switch to #2, to use batts in parallel, turn switch to "both" (or 1&2).
http://www.ebay.com/itm/Blue-Sea-Systems-6007-m-Series-Battery-Switch-4-Position-Selector-Switch-/131262534649?pt=Boat_Parts_Accessories_Gear&hash=item1e8fdb53f9&vxp=mtr