Charge each 6V battery, to exactly the same charge. Let each battery sit for a day or so, and then measure the voltage.
If the voltages are very close, like 6.00 Volt (use multimeter with at least two digits). Then you can make them into 2x 12V systems.
If it becomes too difficult to get them to the same 6.00V charge, (or you do not have a 2 digit multimeter) then once they are very close to the same voltage (within 0.2 volt for instance), then parallel all of the 6V batteries, and let them sit for 24-48 hours or so.
This duration of sitting time, while they are paralleled, will help them get to exactly the same voltage. So after a while they will all (slowly) get to the same 6.00V (or whatever voltage they started out to be very close to, like 6.88 or 5.95 or...)
Batteries that are later connected in series, MUST be at an equal voltage, when they are connected in series. Or one of the batteries will tend to get overcharged.
Like if one 6V battery is at 6.2 and the other 6V is at 6.8, so the difference is 0.6V
and you then push power into them, while they are in series, then the difference between them will remain.
Most modern chargers will provide between 13.8 and 14.6V during the charge cycle. So lets say they get to 13.8V, and thus each 6V battery should be at 13.8 / 2 = 6.9 each.
HOWEVER, because there will still be a 0.6V difference between the batteries, one will actually be 6.6V and the other will be 7.2V.
And 7.2 volt is too much for a 6V battery.
Over charging a battery is NOT a good thing. Especially not if they are sealed batteries anyway.
If they are open cell, then the batteries will go into ''cell equalizing mode', which means that you need to make sure to check water levels and acid levels afterwards.
Sealed batteries must NOT be 'cell equalized' (over charged). As it will create over-pressure, and will cause release of gasses that should NOT be released from sealed batteries. Gasses in sealed lead acid batteries is an integral part of the normal charge cycle, and once they are released into the outside, the sealed battery can no longer be charged properly.
In other words, overcharging a sealed battery (typically to over 14.8V)(or 7.3V for a 6V battery) WILL cause permanent damage to the charge ability of a sealed battery.
So in short.
- Charge the 6V batteries to the same 6.00V charge.
- Parallel all batteries for some time
- then create 2x 12V batteries by connecting 2 6V batteries in series.
When in use. Measure the actual voltage of each 6V battery, from time to time. And if they become too far apart from the same 6.00V reading. Then put the 2 6V batteries in parallel again, and let the get to the exact same voltage again. And then they are good to go back to create a 12V battery again.
Does all of this make sense to you?