How Long to Charge
There is no written rule for how long you should charge a Jet Ski battery. The amount of charge that remains, the number of cranking amps and cold amps and the battery's age can all be factors. Since there's a risk of damaging the battery if you charge it too long, and at too high of a voltage, you should always charge it with an automatic charging station. There are different kinds; find one that charges your battery to its full power and then maintains it with a trickle charge. One such charger is the UPG dual stage charger. Other 12-volt, 2-amp chargers and maintainers will also work. Chargers that allow you to set the voltage and amps and then charge for a specified time should not be used, because an overcharged battery can be damaged or will explode.
Using a Charging Station
Marine stores are the best place to buy the equipment that will completely manage your battery charging. The units cost around $100, and they monitor the battery to ensure the the proper charge is delivered every time. They are simple to use and highly recommended. You can hook up a voltmeter to the battery and read the volts right from it, but this does not tell you how much charge is left--it will only tell you if the battery is completely dead (there will be a very low voltage meter).
Storing the Battery
A battery charging station like the one described will also help you store the battery in the offseason, when it should be fully charged and then trickle charged over the course of the storage season. If you let the battery lose charge for any length of time, it may lose the ability to hold a charge. A battery maintainer will keep the battery charged at the optimum level. If you use a charger without a "battery maintenance" mode or trickle charge feature, then you will have to charge the battery yourself two or three times during offseason storage. Charging it to a proper storage level and keeping it at a precise charge will keep the battery from losing power. A battery stored unattended for the offseason will eventually need to be replaced, and the cost will be very close to that of a charging unit with maintenance feature.