All great questions!
Bobby A, I had the factory speakers installed in the ceiling. They are currently being used. They are too thin sounding for me, so I will probably replace them with Polk Audio speakers that match the center channel.
Cliff, I actually used small square pieces of velcro on the feet of all equipment. Stuff will move around if you don't do this. I've used this technique many times and it works well.
Jim, The Alpine mobile unit powers the outdoor speakers. I can also route the Alpine to two of the ceiling speakers. The white switch allows me to set the rear surround speakers to output the Alpine or the surround channels from the Onkyo. So when listening to TV sound or a BluRay/DVD, the switch is set to the "B" position. When listening to content from the Alpine in the Living room the switch is set to "A" position. The speakers in the bedroom can then be turned on to listen to content from the Alpine.
The iPad (or any USB device) can be connected to the front of the Alpine (as shown). It can also be plugged into the front of the Onkyo receiver which has a front panel USB port. I can stream movies from the iPad (Netflix, Hulu, iTunes, etc.) directly to an HDMI input on the back of the Onkyo. I also use the iPad, iPhone, kids iPod, etc. to play downloaded music and Pandora. I listen to Pandora a lot.
I tried listening to the sub both with the cabinet open and closed. The sub crossover is set at 100hz so there is not much directional sound. The majority of the bass effect gets through the cabinet. There are a ton of adjustements on the Onkyo to mess with the sound which I have tweaked to my liking. The bass of that little Velodyne sub is amazing... and as you can tell fits nicely into the cabinet.
Question for you folks, should I paint those mounting screws black or leave them silver... or am I being too picky?
Be happy to answer any more questions.