If walls and ceiling is open, it is time to wire the heck out of everything. This is very late in the game if you don't have several days before drywall goes up to figure things out.
You can look at a single point solution, or a per-room solution if you want. A single point distributed system is more common. That is you pull speaker wiring to every room you want distributed audio in from a central location, like the family room. If the theater is to get a feed from this system, then you will need to pull a couple of runs of coaxial cable to feed an A/V receiver in the theater for that room's surround system.
I'm not sure how solid the walls are as I'm guessing you can run cabling up and down the walls.
In the theater you MUST run 1.25" conduit from the projector location to the equipment location or you will be in big trouble when (not if) the HDMI cable fails and when you decide to go 4K in there.
But, right now, you have the unique opportunity to wire the heck out of everything. You also should run NETWORK wiring (cat6) around to a bunch of locations. Wireless may be the 'goal' for your phone and laptops, but room devices, whenever possible, should be hard wired to your home network. This takes burden off the wireless network and gives greater reliability and speed to all devices in the system.
If you want speakers in all the rooms, wire for it. It is still typical to have a volume control in many rooms, but if you use a multi-channel amplifier and a streaming device like Chromecast, you can adjust volume at the source and stream music to different rooms rather easily for not a lot of cash.
If you are buying and own this place and plan to be there for 10+ years, then wiring for audio in rooms that you don't intend to put speakers into is a pretty cheap expense right now. You don't have to open up walls or anything, you just run the wire, tuck it into the ceiling, and make detailed notes with photos of where every wire is located. Oh, and you LABEL EVERY WIRE carefully.
