Clayton has opted to replace the factory amplifer with something a with a little more power and sent these photos in.

The amp is an Orion XTR900.2 Two-channel 900-watt amp.
On the left is a Streetwires 4-guage amp installation kit from Crutchfield. On the right is a Install Edge AULOC line level converter.  This will tap into the factory radio's left/right speaker signals and provides line level RCA output for the amplifier.
The subs are two Orion XTR 12s.  Single voice coil and are able to run peak 800 wats RMS.  They are installed in in a R/T box from Best Buy.
The factory radio does not have an accessory (ACC) line.  The aux power drop has an ACC line and this is what was used to turn the amp on.  If you are interested in the aux power drop, there is a How-To article on it.  There is another way.  If you have the factory trunk amp, you can tap into that amp's "enable" line.  It should be the white wire in that harness
Because the 4-guage wire's connector is fastened to the wire at an angle, it won't fit in under the rubber surround for the positive battery fastener.  I had to cut it away with an X-acto knife to fit it in.
The power cable has been covered with a wire loom and tie-strapped in place.
The cable goes through the firewall using an existing grommet and comes out under the dash area.
Power cable went under the plastic moldings.  They come right up if you tug on em, the real problems were the B-pillar moldings that had to fit over weatherstripping on both the front and back.
Installed the ground wire from amp in trunk to chassis behind fold-down seat.  Pretty simple, just drilled a hole and put a screw in to hold down the ground connection.
View is from the passenger compartment with the seats folded down, looking at the back of the speaker box.
The line level converters tap into the factory amp output and tucked up into the package shelf.
Completed install.  You can see the amp above the box.  The box doesn't cut down on trunk space too drastically.  The box is about 3.4 cubic feet.  Each sub needs only 1.5, so counting all the board, it shouldn't be too far off.

A couple of issues came up during this install.  Initally, Clayton installed the line level converters behind the head unit however nothing worked.  He moved the converters to the trunk and tapped off the output of the factory amp and got the system to work.  I believe the system would have worked as he originally installed it if he unplugged the factory amp.  According to the service manual, the amp sends a signal to the head unit to drop it's output to line level.  If the amp is not installed, the head unit boosts the output to speaker level.  Since the factory amp was left in place, the head unit's output was line level.  So the line level converters were dropping line level inputs to sub-line level outputs.  Actually, if he tapped directly from the factory amp input and left the amp plugged in, I think he could have left out the converters.