I've seen quite a few people coming to this site with search queries identical to this article's title. Since there is nothing explicitly written anywhere on how to charge two 12 volt batteries with a single 12 volt battery charger, here you go. Really, it's quite simple, but there are a few "best practices" to keep in mind.
The first thing you need to do is to take the batteries out of the vehicle. It's not actually a strict requirement, but it's a very good thing to do. You don't need to mess up your vehicle electrical system, and if you've got two batteries, who knows how they're connected, what they power, if you have a charging isolator, or other complications.
Now that the batteries are safely on your workbench, connect them together in parallel. Take a set of jumper cables and connect the positive terminal of one battery to the positive terminal of the other battery. Do the same for the two negative terminals. Remember to keep things simple - the red goes to positive, the black goes to negative.
By connecting the two batteries in parallel, we are allowing the charge between them to equalize - if one battery is charged more than the other, then the excess charge in one will be driven to the other, until the charge (measured by voltage) is exactly the same on each battery.
Be sure not to connect a completely dead battery to a fully charged battery. The amount of differential voltage can tend to send a large amount of current (amperage) to the dead battery, causing a significant amount of heat to build up. This is a bad thing and should be avoided. If you have a completely dead battery, charge it on its own before connecting the two together.
Finally you need to connect your battery charger. Now here's the trick: don't just connect the charger directly to one battery. Instead, connect the positive lead from the charger to the positive terminal on one battery, then connect the negative lead on the charger to the negative terminal on the second battery. This is a small detail, and in truth makes only a bit of difference.
Turn on the charger, and let it do its thing. Remember to select the correct amperage on your charger for you battery type (although not all chargers give you the choice), and also remember that you'll need twice the time to charge two batteries in parallel as you would need to charge a single battery.
We hope this helps - have more questions? Ask below and we'll see what we can do!