There are a couple of precautions to consider with charing a deep cycle battery using a vehicle power supply circuit. First, as mentioned, a depleted battery can put a big load on an alternator, which isn't designed for such high peak current. You may damage the regulator and/or the diodes in an alternator unless you use an in-line current limiter on the charging circuit. I like to put a headlamp in series with the battery to keep the current flow at less than the max rated for the alternator circuit, although doing so will make the charge time longer, as it should be.

Another big consderation is the differecne between the make up of a deep cycle battery vs an automotive battery. Vehicle electrical charging systems are built so that the battery is constantly floating on a charge voltage, allowing a trickle charge to be constantly applied to the auto battery. This trickle charge keeps the battery at full charge, but a fully charge deep cycle battery is not made for this type of operation, and will fry if left to float on a trickle charge circuit. For this reason, once a deep cycle battery has reached full charge, it needs to be isolated from the vehicle electrical circuit. Again, having the headlamp in the charging circuit is a great aid for this. As the battery charges, the voltage drop across the lamp decreases, and the lamp gets dimmer. When the lamp is no longer putting out light, the battery is fully charged and can then be switched out of the circuit. An ammeter is a better indicator, but for the basics, this has been a good standard for battery charging for a long time.