Ill be doing a pull down screen this year with basic HD projector (TBD). If I were you id just put a retractable screen in the main downstairs family room above the fire place, and just make that your theater room and keep the other room as storage/work shop.
For wiring, youll need to run whatever your system will support. At min id run Cat 6 cables, good speaker wire to all locations, HDMI cables, and rca cables if you need them run to a cabinet thats going to house your stuff.
Theres a free 50" rear projection TV on mnaudi if you want a good deal!!