Pre-Construction Speaker Locations

since you are still in the early stages of construction, "in-ceiling" units are the least desirable method of locating speakers. By all means, if in-room speaker enclosures are not desirable, then in-wall units are much preferred over in-ceiling speakers. For the front 3, it is much better for the soundfield to come FROM the TV area than from the ceiling.

Media Room: please consider in-room speakers for at least the front three and subwoofer(s). In-wall units for the sides in 5.1, or for the sides and rear speakers in 7.1
Prewire the projector location for AC power, an HDMI cable, and just "in case", component (red-green-blue) cables.

Family room: please don't consider mounting the TV over the fire place (common mistake). Attempt to lay out the room where the TV is on the large wall. Yes, good in-wall speakers would work for the front 3, and in this case because of the lack of convenient walls, in-ceiling units with pivoting tweeters (aim towards main listening position) would be OK. In-wall subwoofers are available as powered or passive (an additional subwoofer amplifier is required at the equipment location) units. You might consider two smaller units instead of one large subwoofer. In room subwoofers may perform better, but WAF may nix that.

Specify at least 14 ga. CL2/CL3 in-wall wiring - pre-locate where you want the in-wall speakers and either use pre-construction templates mounted prior to drywall or carefully locate where the wire drops will be hanging behind the drywall so your cut-outs for the speakers will be in the correct position to retrieve the speaker wire.

Dolby Labs recommends all front speakers (really the tweeters) be at seated ear level, and the surrounds be at slightly above (whatever that means) seated ear level. If you use an acoustically transparent screen in the media room, you can line up the speakers with the center behind the screen. If you use in-room speakers this will still work if the screen is located out from the media wall. In the case of a large flat screen HDTV, locating the center channel immediately above or below the TV will work fine.

good luck

do a quick layout on the equipment and seating for the media room. Consider where the equipment center will go so you can home-run all the speaker wiring there. If you are going to drywall in the media room, then running the wires for the surrounds to just hang down into the wall cavity....or terminate in single gang boxes with flat cover plates should be very inexpensive - much easier when the wall is open than after it is drywalled. Make carefull notes as to where the speaker wires are so you can find them later if you don't use single gang boxes.

Wiring to the projector - depending on which way the floor joists run (across the room or parallel to the long dimension of the room) getting wiring into the ceiling area after drywall can be extremely hard (joists that run across the room would need to be drilled to pass the wiring). At least prewire an in-wall rated HDMI cable from the equipment center location to the projector location, along with an AC power outlet (do not allow the installer to run the HDMI parallel and close to the AC line feed - you will pick up interference on the HDMI cable). This little bit of prewiring will save you ton's of problems later. Another option, but could be more expensive, would be to install a 1.5" conduit (with pull-cords left in the conduit) run from the equipment center site to the projector mount site, for wiring later.

This might sound silly... but from a 'done a tonne of network wiring standpoint' make sure you leave a few fish strings in the conduit to make your life easier down the road when you want to pull additional wires (not having to unfish a wire with a string attached, then re-fish 2). This makes changing what wires are run where a nominal task rather than a weekend killing enterprise.

(standard disclaimer, I know nothing of your wiring background, and this is common to people who work in it, but not common sense to everyone)

There is nothing worse than seeing blanks plates on your ceiling. Have the contractor, hopefully an actual A/V dealer and not the GC, zig zag the line back and forth between the 2 joists or studs where the speaker will be going. This leaves a nice smooth ceiling if you don't put speakers there now, allows plenty of wire to connect when you are putting in speakers and will allow you to place the speakers in different locations within the stud or joist.

Just make sure you take pictures where the wire is prior to drywall. Or if you don't, a tone kit will find the wire in the wall anyways, it just takes longer.