First, remove the positive and negative cables from the batteries. Put an Ohm-meter across the positive and negative cable. If your reading is close to 0 Ohms then you have a direct short.
Next, do a parasitic draw test. Make sure your battery is fully charged. Check to make sure ALL loads are turned off. Unplug anything you may have plugged into the cigarette lighter. Remove your keys from the ignition. Close all doors so the dome lights are off.
Disconnect the thick positive (Red) cable that goes down to the starter.
To start make sure your meter is set to the 10 amp DC range. Some meters have a special connector for the red probe when you are reading current. You can either do this next step by just holding the meter probes to their respective contact points (you won't get a shock from 12 volts) or you can use probes with alligator clips to snap them in place so your hands are free to do something else.
Connect the positive probe to the battery - either battery is fine, electrically speaking, since they are connected together by the negative (Black) wires. Polarity on digital meters doesn't matter because they are autosensing.
Connect the negative probe to the red cable that is still connected to the vehicle. Make sure this cable and your probe do not touch ground.
If there is a severe current draw (more than 10 amps) it will either pop a fuse in your meter or destroy it outright. That's why you need to test for a short, otherwise, your meter should now be reading the current drain on your battery.
If your vehicle has an alarm system or remote locks, the current draw may be around 2-3 amps for a few minutes after you last close the door. This is normal. If you're not sure, wait at least 20 minutes after you last open or close a door before you take a reading.
If everything is normal, you will read less than 35 milliamps, or .035 amps. If the current drain is higher than that, you need to find out what is draining your batteries: You can start by pulling fuses until the load goes away. If that doesn't reduce the draw, you need to look for a wire that is corroded or frayed.