Problem with 6 volt batteries in series vs a 12v battery, or in the case of 2 12v batteries in parallel is the available current which is partially limited by the batteries internal resistance.
Internal resistance is realized by the difference between the terminal voltage of a battery at rest, vs a battery supplying current to a load. Older and more sulphated up the battery, the worse the internal resistance.
Example: Using round numbers, a fully charged battery reads 12v terminal to terminal. You push your start button and your battery is required to supply 100-150-200 amperes to the starter. Measuring the terminal voltage of the battery under that load and using ohms law tells you what the internal resistance of the battery is.
Ohms law is the association of voltage, current and resistance in an electrical circuit. For DC (direct current circuits, like battery circuits) current flow (which is what does the work) is the result of available (applied) voltage divided by circuit resistance; voltage is in volts and resistance is in ohms. An ohm is defined as a voltage drop of one volt across one ohm of resistance with a current of one ampere flowing.
So if you have 100 amperes required (small engine) to roll your starter and each of 2 6v or a single 12v battery have an internal resistance of 0.01 ohm, the voltage dropped across the battery for the 6 volt pair would be:
IxR =V drop. So for 0.01 ohm (which is nothing) at 100 amperes you would have 1 volt dropped across each battery for a total loss of 2v. Meaning the resultant available voltage to roll the starter would only be 10v. Butttttt 10v is needed AT the starter and you have wiring losses between the battery and the starter.
However, the 12v battery would only have one loss of 1v and would have 11 v available to spin the starter meaning it could accommodate 1v of drop in the wiring between the battery and the starter and still be able to supply the minimum voltage of 10v to the starter.
If you used 2 12v batteries in parallel (side by side, + to + and - to -), you would halve the resistance loss and would have 1.5 volts available for the wiring harness loss.
I had a 4230 JD tractor. Had a 6v on each side of the tractor wired in series.....like you are wanting to do. In short it was a dog to start.
I replaced the 6v batteries with 12v which were of the same physical size, wiring them in parallel (as described above) quartering the resistance rather than doubling it. I guarantee you that diesel would start before you could turn the key loose and at anything above 20 degrees you needed no starting aid.