I am a little confused by your comment " the Triton doesn't have an alternator and requires a trickle charge every 3-4 trips" ?
Whatever outboard motor you're running surely does have a charging system and should be keeping the cranking battery charged to the proper voltage if you are using the boat on a regular basis. Perhaps there is a problem with your outboard's battery charging system output and that is why someone connected one of the trolling battery charger outputs to the cranking battery. Normally each set (1 positive& 1 negative ) from the trolling battery charger outputs are connected to the pos & neg terminals of each battery . If the batteries are properly connected in "series" for a 24 volt system but only one battery is being charged once the battery without any charger connection goes dead you would be left with only 12 volts.
The total voltage of the series connected batteries would be 12volts
(battery on charger) + 0 volts (uncharged dead battery)for a total of 12 volts. You need to verify the connections between the two trolling batteries and the voltage of each battery. A low cost DC voltmeter would be a great help in trouble shooting this problem .
When you start your outboard you should see an increase in the battery voltage of the cranking battery if the charging system is working properly . Same with the trolling motor batteries once you plug the onboard charger in . Hope this helps