Use another set of cables to connect the open positive and negative terminals to your application. They can have different capacities on account of size or age but the same chemistry eg.

Solar Ray Wirediagrams
Charging 3 12v batteries in series. By charging 6 volt batteries in series with a 12 volt charger you allow your off grid electrical the true capacity it needs. In theory a 6 volt 3 ah battery and a 6 volt 5 ah battery. All flooded lead acid or all agm. Turn on your charger ensuring it is set to charge at 12 volts. To charge two 12 volt batteries in series youd need a 24 volt charger. When charging 3 12v batteries in series with one another each voltage of each battery would increase in an amount dictated by ohms law v ir for voltage v in volts current i in amperes and resistance r in ohms.
For a plethora of information. How battery charging works with a parallel battery bank. Voltage if there is one. Connecting batteries of different amp hour ratings in series. Others have a meter that shows the charge rate and once its near zero your batteries are charged. Let your batteries charge until the charger indicates they are fully charged.
A 12v agm battery on average has only 150. Thats the pat answer. The easiest way to fix a voltage difference is to charge the pack fully then bring up the lowest battery with a 12v charger placed on just the lowest battery. This makes charging the battery difficult because the increases in voltage will provide different charges to each battery. In theory a 6 volt 5 ah battery and a 12 volt 5 ah battery. Some chargers have a light that illuminates once charged.
To connect batteries in a series use jumper wire to connect the negative terminal of the first battery to the positive terminal of the second battery. Of the smaller battery through the over discharging and over recharging described and shorten the life of the larger battery through under charging. You do not need to disconnect the series connections to do this as long as you can access just the lowest battery. Plug in your charger to the electricity supply. Charge more than five batteries by connecting one 12 volt battery charger across each battery in the series as if each battery were the only one being charged. Two 6 volt batteries in series vs one 12 volt life cycles.
Charge all the batteries at the same time. You need to overcome the total voltage of the series batteries 12 v 12 v 24 v to drive. 6 volt agm battery has more life cycles. Lets suppose you have 3 different 12v batteries wired in parallel to supply 12v power to your rv. Discharging down do 80 depth of discharge 600 700 on average. Next time you charge you should see the batteries are then closer in voltage at the end of the charge cycle.