I know this may seem really silly, but my husband and I are new to outboards, let alone pontoons. Do they have an alternator or some kind of recharging system for the battery???
Generally speaking, if the motor has electric start and is a fairly recent model, it will havea charging system. But knowing your particular model would help..
Look at the instrument panel? Do you see a "Voltmeter". If you do, there is a good chance the engine has an alternator. If not, you will need to tell us what make, year, and HP engine you have.
DO NOT run the motor without a battery attached. Do not disconnect the battery once the motor is started. If you have a battery switch, do not switch off the battery with the motor running. Any of these will fry your alternator.
(again, just in case, better to be safe than sorry)