No, not if the motorcycle is wired for a 6 volt system. This must be a very old motorcycle.
Usually 12 Volt
All Harley Davidson motorcycles have used a 12 volt battery since 1965. Prior to 1965 they used a 6 volt battery.
Motorcycle batteries may be 6 volt rather than 12 (check this) and if they are 6 volts, switch your battery charger to 6 volts or you may damage the battery.
Very gently. A motorcycle battery can't take as much charging current as a car battery, so you need to use the lowest setting on your charger.
Unless it's an old vw bug, cars usually run on a 12 volt dc system nowadays. Motorcycles often run on a 6 volt dc system. Different systems require different charging voltages so you won't ever be able to charge a 12 volt car battery from a 6 volt motorcycle battery charger as the output voltage would be way too low. However, if you can set the battery charger's output to give either a 6 or a 12 volt output, then you must always remember to set it to 12 volts if you want to use it to charge a 12 volt car battery.
Any good 12 volt battery charger that puts out around 10 amps. Make sure it is an automatic charger. The same charger you use on an auto battery can be used on a motorcycle battery.
No, a 12 volt 12 amp deep cycle battery will not keep your motorcycle running. A deep cycle battery is one that can survive repeated deep discharge cycles. As the voltage reduces, however, your motorcycle may stop operating correctly, because it is not designed for this type of battery. The proper solution to your problem is to fix the cause of the charging system problem in your bike. Besides, if you check the specifications on the required battery, you will probably discover that it is rated for much more than 12 amps.
Charge it with a 12 volt battery charger.
It depends on how the two six volt batteries are connected. If they are in parallel then the answer is no. If they are connected in series then the answer is yes. To find out for sure check the voltage that the starter needs. If it says 12 VDC then you will know that the two six volt batteries are wires in series and can be replaced with a 12 VDC battery.
No
12 volt
1.250 specific gravity maintenence free battery uses 1.320 gravity