You need to do a total room layout first. Decide where the screen, seating, speaker location, and all your equipment (DVD Receiver etc..) will be located. If passable hook up your equipment temporally and try out these locations before the sheet rock goes up. It is much easier to move items at that time.
Run a dedicated circuit from you electric panel to your equipment & sub locations.
Your equipment area should also get an antenna, or cable wires needed plus a network wire for a computer if needed.
Run 12 or 14 to all your speaker locations. Decide if your are going 5:1, 6:1 or 7:1.
The LFE wire to the sub and 110.
Your from your equipment to your projector, I would run composite, component, S-video and HDMI. The projector will need 110 also, some projectors you need to put a switch on it.
Sorry about your flood, I had a small flood last April.
The Trilogy It took 5 months to rebuild and remodel the house. Kind of a blessing in disguise. The house is better than it was before & the theater is twice the size.
