I think the subs firing off the back glass is the best IMO.
The glass creates a sonic resonance, and can cause distortion when the two sound waves intersect each other. One thing to remember about sound waves, they are NON DIRECTIONAL. You can face your subs and which way you want, but the sound originates from the sub and radiates outwards. Moving the box around only affects the reflection of the sound waves. So, its not weather they are facing up, or facing forward, its what they are facing towards that makes the difference.
I'm getting an 18" Resonant Engineering SX (not released yet, starts production thursday) and powering it with a HiFonics Brutus1500D, 1500 watts RMS @ 1 ohm.
How do you plan on running a single sub at 1ohm? What's the speakers ohm rating? DVC/SVC? How much airspace does it require? Building a box for an 18" sub means the face has to be 2 pieces of 3/4" MDF, face to face and glued together -- otherwise the weight of the speaker will crack the box. Remember that the Cougar only has about 4cufu of airspace in the entire trunk (including using the sides, and spare-tire well.)
Btw, there is a reason that competetors generally use 12" subs. When you go with a larger sub, the power required to produce the same sound with a smaller sub is increased exponentially. Here's an example, using numbers pulled outta my ass:
10" creates 100dB @ 100watts
12" creates 100dB @ 150watts
15" creates 100dB @ 250watts
Now, as you can see, the bigger the speaker, the more power required to drive it to the same performance of a smaller speaker. (More voicecoil to move around.) Now, you can get MORE sound out of a larger speaker, yes, but it requires double the power. I have proven this over and over again in competitions with some of my outlandish setups.
For example, my 24 8" Subs w/ 25 watts each was MUCH louder than my 16 12"s. (Each had 192" of cone-diameter.)
E1