This describes the installation of a backup battery system into a 2007 Toyota FJ Cruiser named Suzie. Such battery systems are often used in vehicles that will be used off road, have extended electrical needs for high-current-draw devices such as winches, or will have radios, lghts, etc. used for extended periods with the vehicle parked (i.e., with battery not being recharged).
There are several ways to connect a 2nd battery, from simple parallel installations to manually-switched systems, to more elaborate automated systems. I chose to use a BIC-95300A automated system with an in-cab remote switch from Hellroaring, Inc. I used a previous version of this device in my old Tacoma and was pleased with it, so chose to again buy a Hellroaring product. For some of the advantages of their systems, they've got a chart on this page. (I am not affiliated with any of the vendors I link to on this page).
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Where to put the second battery was made easy by the FJ's engine compartment layout: with an AirRaid intake replacing the stock air filter intake, there was only one logical place to put the battery tray: passenger side, up against the firewall. I had a steel tray attached to the engine bay frame using fabricated brackets by the guys at John's 4x4 here in Boulder, CO. The Optima Yellow Top battery I chose to use is a dual-purpose starter/deep cycle type battery that is capable of both providing high current for starting purposes and being drained deeply for extended use.
A view of the battery location as seen from the passenger side of the engine bay:

The backup battery must be connected to the vehicle's ground, so a cable was fabricated and connected to the chassis at the point shown below. Note that once this connection was made, I used a multimeter to check that there was a good connection between the battery's ground (-) post and the vehicle chassis and the main battery ground (-) post.
Ground cable connection:

The BIC units from Hellroaring are small and come with extensive installation instructions and documentation. They are also flexible, and can be rigged in multiple ways or various uses; I'm using the "standard backup setup" recommended for offroad use. For details of various setups, see the application notes on Hellroaring's site.
Below you can get a sense of the BIC's physical dimensions. It's something like 3.5" x 4" x 2"h. On the device are connections to the backup battery, main battery/alternator (which allows the backup battery to both recieve and provide current), vehicle ground, as well as connections to the remote in-cab switch that controls the system's function.
Detail of connections on the BIC unit:

Here you can see the cable I fabricated to connect the main battery to the BIC unit. It's run back towards the firewall, then attached using zip ties following the same pathway as the factory wire loom in that location. Note that in the final configuration, the cable doesn't block acess to the fusebox as this picture suggests.
Main Battery to BIC Cable:

Hellroaring offers this three-position switch as a convenient way to control the BIC's function from within the vehicle cab, regardless of the BIC's physical location. In my old Tacoma, this was important because the BIC was installed in an inconvenient place in the rear bed of the truck; in the FJ it keeps me from having to even open the hood when using the backup battery.
The switch has three positions: 'off' (BIC not used, backup battery disconnected and not charged), 'auto' (no current draw from backup battery, backup battery charged by alternator just like main battery), and 'connected' (backup battery joined to main power system, current draw from backup battery possible). Note that I used a household label maker to make little labels for the switch to remind me of which position is which; normally the LED lamp is enough of an indicator.
I chose to place the switch next to my PIAA fog & driving light switches. I probably should have placed it a little further down to avoid interfering with fuse panel access, but it's not really a big deal.
Detail of BIC remote switch:

The remote switch must be grounded; I did to using a convenient ground point behind the kick panel. There are three additional wires that must be routed through the firewall to the BIC unit. I chose to use the same hole I had drilled for routing the PIAA light's wires. This hole has a rubber grommet in it to prevent wire chafing against sharp metal.
Detail showing BIC remote switch wires entering engine bay through firewall:

Where to put the BIC? It has four screw holes at the corners; in theory it could be mounted in many places. Due to some future plans I have for items that will be installed in the engine bay, I didn't want to assume that any given location would remain unblocked, nor did I want to have to re-fabricate any cables when those items are installed. I chose to mount the BIC atop the backup battery itself, using some thin wood sheeting attached to the battery tie-down rods (and leaving the battery vent holes unblocked!).
Now that the BIC was mounted, I knew how long the cables to the main battery and remote switch needed to be, so I finalized routing of those cables, using zip ties to keep things tidy and shortening the (+) cable by a foot or two to avoid clutter.
Detail showing final BIC location, mounting & cable routing:

Another view of the battery & BIC, with cable routing:

More detail of the BIC mounting. Note the unblocked vent holes on either side of the battery and use of cable conduit (included with remote switch kit) to keep small wires tidy:

Finally, I wanted to protect the top of the BIC and the electrical connections on it. In theory, I could have mounted the whole affair inside the cab, leaving only the battery itself in the engine bay, but if I'm ever in water this deep, there's already water inside the main fusebox, so I'm mostly concerned about water dripping from above. The sealing of the engine bay hood is very good, and this location appears to not be very splash prone, but a thin sheet of plastic is cheap insurance. So using the BIC's center terminal, I attached a thin sheet of modeling plastic from the hardware store to cover the BIC unit.
Picture showing final mounting & BIC cover:

I haven't needed to use the backup battery in the FJ yet. In my old Tacoma, it came in handy many times when the main battery had, for one reason or another, become too drained to start the engine. I was able to use the remote switch to engage the backup and be on my way.