How are you charging the 2 systems?
Bad way:
Have a 3rd battery for 12V accessories. Wire it in parallel to your starting 12V battery, but isolate it with a battery isolator. It will charge with your 12V starting battery, but your 12V and 24V batteries will quickly become unbalanced. Not recommended
Better way:
Same as above (3rd battery with Isolator), but use a battery equalizer between your 12v and 24V starting batteries. This is what I do, and it works ok. But, my 3rd battery is an AGM, and it never really charges, because AGM's want really high voltage to charge properly, and you just can't get that from an equalizer.
Hint... some isolators have a override option... with this set-up, you can back-feed from your house battery, through the equalizer, to help your starting batteries if they've gone dead for some reason. Shaker has started his truck this way on at least one occassion.
Best Way: buy a DC to DC charger, like this top of the line
Redarc, but other brands are available. The Redarc in particular, will take 24V from your truck, and both isolate and properly charge and maintain a 3rd 12V battery, including AGM's. This is the right and proper way to have a 3rd battery. Run all your 12V accessories off this battery. If you add two 24V solendoids you can have continupus, switched 'Accessory' and 'run' 12V power.
Yet Another clever way: Awlteq used some spare room on his 3B engine to install a 12V alternator dedicated to charging his 12V 3rd batteries.