While it's nice to talk about wiring everything everywhere, it's extremely cost prohibitive to do this.
Wiring in family room: Are there rooms above your family room? If yes, then under NO circumstances do you want in-ceiling speakers! Think about it for a second and you will understand why rooms above would make this terrible. Second is up! In ceiling speakers send sound downward into the room, but also upward to the room above. Almost as much sound goes both ways, so under no circumstances do you want to do this. Instead, you want to go in-wall, or better yet, in room. This is a personal choice and you get more quality with in room speakers such as floor standing or bookshelf speakers than you do with in-wall speakers. But, giving the choice of in-wall or in-ceiling only, go in-wall. You get better sounding options, great isolation, and better placement. But, if you go with floor standing or bookshelf speakers, then have wiring pulled to standard outlet height (12" or so from the floor) and have a set of binding posts put in the wall at that height. This means, you need to plan accordingly for the left/right speakers. You may want to go on-wall for surrounds, so if the room supports this, then put them at the proper height on the wall. For the center channel, you may want something wall mounted, but it depends on where you are putting your components. There's a lot of thought in this one room, so feel free to discuss just this room at length and what you want to accomplish. Where equipment will go in relation to the TV, etc.
By example, my family room TV is on the wall (hung). My center channel is wall mounted directly beneath it. My left and right speakers are floor standing, and the speaker wire was brought through the carpet to connect to the bottom of the speakers directly. I have a subwoofer which I put behind the couch. The room only would support the surround speakers if I went in-ceiling, so I don't use surround speakers. Instead, my surround speakers will be in my basement/home theater setup. All the equipment for my family room is in a rack about 15 feet to the left of the TV. I have basement access (for now) between the TV location and the rack location. (it's actually a lot more complex than I am describing, but close enough for comparison)
For upstairs, if this is a better room for sound due to the size/shape, then the same rules apply. Still, if there are rooms behind the walls you would put speakers into, then in-ceiling is a better choice than in-wall. Floor standing or bookshelf is still the better sounding and isolation option. I use in-ceiling speakers with angled speakers in all my upstairs rooms. None of the rooms are dedicated spaces where better sound would significantly benefit the space and the angled woofers with the speaker wiring close to the front of the room works well. But, in a dedicated space I would try for in-room speakers of some sort if at all possible.
I would (and did) wire the home with cat-6 for networking. If you have a equipment location that is not accessible and is not near the TV, make sure to put in 1.25" (or larger) conduit between the TV location and the equipment location.
Considering such things as whole house wiring, and planning for future upgrades. If you have a basement in the home and it is unfinished, or if you have a decent crawl space, than that's great as it gives you access to walls on both floors after construction is done. But, if you have a finished basement, then a great deal more thought should go into the whole house wiring setup, location of equipment, and a whole lot more.
