The second battery is for cold climate cranking amps and the additional draw from glow plugs intake heater and fuel heater.

Replace it your gonna need it

 

replace both,or you will have problems again.then you will be right back to buying two anyway's.1 older battery will not be able to hold up the same voltage as the new one,there for it will alway's be dischaging your new battery.and like the other member said,two batts are because your glowplugs probably use almost as much power as your starter,and when it's really cold they need to be on for 20 or 30 seconds or more before you start truck.
the batts are paraleled,not in siries like big rigs.in series would make 24 volt's,we have 12 volt systems.

 

Could you put a isolator kit on that would allow you to jump the first battery from the second one? More just for emergency cases than for regular use.

 

These batteries are connected together at all times, there is no primary and backup, it's just like 1 really big battery. One bad battery can take down a bank of them. If you would have just disconnected the bad one the other would have started the truck. You should replace both, as others recommended, before winter. I'd do it asap.

 

Could you put a isolator kit on that would allow you to jump the first battery from the second one? More just for emergency cases than for regular use.

Can you? Yes. Should you? No.

Dual battery system is necessary to supply power for the glow plugs and air intake heater, plus turn over an engine with something like 22:1 compression ratio. The purpose of using two batteries is to supply the needed amps - not voltage.