Deep cycle batteries are best charged using a multiple stage charger. I forget the specifics but hunt he net. A cheap single stage charger or the alternator is not the way to go for long deep cycle life.
DO NOT USE A SINGLE STAGE!!!. I use a two stage and that's supposedly not optimum but I get 4 seasons out my batteries (I run 2 dual purpose batteries). A single stage will not adequately charge deep cycle batteries. Deep cycles need a low & slow charge for about 22 hours for a #24 battery.