I have a 16ft Tracker boat with a 9.9 horse Mercury. Instead of the deep cycle battery and starting battery, I wanted to just have 2 deep cycles for when I go for long weekends without any way to recharge. The deep cell will start my little motor, but if it's hooked up to the motor, will the alternator/charger in the motor do damage to a deep cycle battery? The guy at Bass Pro wasn't sure, but said to just disconnect the battery after starting before running up the lake. I can start my little motor with the pull cord if I want, and just keep the extra deep cycle as a backup, but I don't really want to be screwing around with wires every time I start and go somewhere with the gas motor. Anybody got any input?

Sounds like your 9.9 motor is the 'little' motor and main power is something else. If you previously had a cranking battery to start the main motor and it was being charged by the alternator, a deep cycle battery should be OK as it uses the same charging method. Your alternator is not likely to put out more current than the new battery can tolerate. The deep cycle battery will not have as much cranking power, but if you are using an outboard of less than 150 hp, it should be enough. I am puzzled why the bass pro guy was concerned. Alternators routinely charge batteries and the problem isn't obvious to me. Perhaps other guys have had some experience with this application of deep cycle batteries.

You won't run the outboard long enough, if you are a bass fisherman, to get much benefit from the 9.9 alternator if your engine has one. I have a Tracker 170 with a 9.9 Merc 4-stroke electric start and it barely re-charges what the electronics use in a day's fishing. I use a deep cycle battery for it and for an electric motor when I fish electric only lakes. The 9.9 alternator won't damage your deep cycle as it is only a 6 amp.