Here is a decent explaination from another member lifted from another dual battery thread:
Here is the deal on the optional FACTORY Aux battery on a gasoline powered van works, well at least my 2008 V-10. I just added a second aux battery with a tray I bought from e-bay. Here is what I found out.
The option Code is 634 $145 in 2008 you got ONE 78 AMP battery (main) and ONE 75 AMP battery.
The battery IS isolated from the main battery when the key is off.
The battery size is group 65 for BOTH of my Batteries.
The biggest problem of the batteries are how tall they can be and still fit in the box. 6 1/2 inches tall is it, unless you modify the box.
Aux batteries are available WITH and WITH OUT a trailer package.
Aux battery powers the trailer battery relay (if it has the FACTORY hitch wiring installed) when the key is on or off just like it does if you don't have an AUX battery but if the trailer drains the battery with the AUX battery the van will still start.
The relay for the Aux battery is mounted under the main battery.
The part number is F8UB-14088-AA
There is a diode in the hot in run circuit, it is mounted in the (as Ford calls it) BJB or battery junction box next to Fuse F5.
This wire on my van is White and Black 14 or 16 gauge and hooks to the small/energizer terminal of the relay.
One of the large terminals on the relay is another Black and White wire. This one is 8 or 10 gauge and hooks to a 60 AMP Fuse F20 in the BJB. This wire is Hot all the time.
The other large terminal has the feed wire to the Aux battery and a Red/Yellow wire that
feeds the trailer relays via BJB Fuse F24 20 AMPS and Fuse F8 40 AMPS.
(note without an Aux battery these two large wires have a jumper in them in at connector C145)
I hope that helps any of you who have wondered how this all works. I spent many hours with the factory Ford wiring book and a volt meter making sure this is how it works before adding my Second Aux battery to my system. The manual makes it look to me like the relay should have four terminals but mine only has three.
Oh and the reason for disconnecting the Aux battery ground (at the frame connection) is because it DOES power the trailer relays all the time even if the other battery is disconnected completely, plus one terminal of the relay is still hot.