When you have a dual battery system in your vehicle, there are two ways to charge both batteries. You can either use a dedicated charger or an automatic switch. A dedicated charger will charge both batteries at the same time, while an automatic switch will alternate between the two batteries, charging each one individually.
If you're using a dedicated charger, simply connect it to both batteries and let it do its job. If you're using an automatic switch, it's a little more complicated. First, you'll need to identify which battery is your primary and which is your secondary. The primary battery should be the one that's connected to your engine starter and alternator, while the secondary battery should be connected to accessories like lights and radios.
Once you've identified which battery is which, simply connect the positive terminal of the primary battery to the positive terminal of the charger, and then do the same for the negative terminals. The automatic switch will take care of the rest, alternating between charging each battery individually.