No, if they are wired in series you have 36 volts assuming each battery is a 12 volt battery. They will have to be wired in parallel to output 12 volts. In that case you can charge them with a 12 volt charger but it will take 3 times as long as charging just one 12 volt battery.
No, not if the motorcycle is wired for a 6 volt system. This must be a very old motorcycle.
No. You can only charge one 12 volt battery at a time or two 6 volt batteries wired in series at a time if you want to use that 12 volt charger.
As long as the ATV is wired 12 volt, not 6.
You would wire them in "Parallel". That means positive post to positive post and negative to negative. Two 12 volt batteries wired this way doubles the capacity and amperage capability of the system. It does not cause any harm to the electrical system as the system sees them as one big battery.
No, but you can charge each one individually without separating them from the series loop.
You'll have four 12 volt batteries wires in parallel.
If it is a 12 volt marine battery, then yes. If it's a 6 volt marine battery, then you would need two of them wired in series to make the 12 volts needed to start the vehicle.
No, since in series they are 24 volts so you need to charge each one independently with the 12 volt charger. This may be done disconnected or leave them connected and put the charger on the + - of the same battery.
If a single 12 volt source as in 2,6 volt batteries wired in sequence or one 12 volt battery can be isolated from the system it is possible.
That depends on how the batteries were wired, for what voltage. If they were to provide a 6 volt source, then yes, but not for very long as the 12 volts would burn the motors out very quickly. If they were wired to provide for 18 volts then yes, but it won't run very fast because of the low voltage.
Depends on the amperage of the batteries you are using. Both setups will give you 36 volts, but you will normally have a longer run time with six 6 volt batteries in series than three 12 volt batteries. That is why golf carts use 6 volt instead of 12 volt batteries.