I have a new 2013 Ford Explorer with the same keyless ignition. I have the hot wire from the MH plug connector wired to the hot side of the Explorer battery through a "toad charge". I have about 5000 miles towing the Explorer without problem. I do run the Explorer a couple of times a day if we are going to be traveling more than 6 or 8 hours but other than that no special precautions. First thing before traveling i run the engine for 10 minutes or so and then put the transmission in neutral after shifting through drive and reverse as required by ford. I then lock the doors using the door keypad, take the key with me and the the computer kills the electronics after 20 minutes (again as stated in the manual). I also have the AF1 braking system.
If you have a direct hot wire to the MH without the toad charge you can have a drain back to the MH when the rig is parked w/o either motor running depending on how the MH is wired. The tail lights on the toad can also be a drain on the battery depending on how it is wired.
i have never had a dead battery after installing the toad charge even after several days of towing in this manner. First trip out i did have a dead battery w/o the toad charge but only then after two long days of travel.
I would check to see if the hot wire from the MH is actually charging the battery on the toad.