I would run min. one coax, one cat-6 to those locations such as bedrooms, office, kitchen. For every point that telephone is going to connect, at least two cat-6. For where the main components are going in the living room, no less than six cat-6, and no less than two coax.
Pull everything, I mean all coax, ethernet to a central point, where you can place stuff like a patch panel for both ethernet & coax, rack mounted switches, telephone & ISP equipment, and also if going to be running a server, a shelf for that, or use a rack with a shelf, and also make plans to have a monitor & keyboard and mouse for that point, so if you are in there making changes to the network, you can do it there vs. through a app such as Teamviewer.
As long as you have a copy of the Blue Prints, it makes things easy, because you can lay tracing sheets over to make changes for the low voltage systems, and use colored pencils or markers, along with a key, so that it makes it easier for you to know what is what, when you look at your notes & the schematic.
As for marking what is what at the patch panels, or keystones, just mark with the number on the keystones where they land on the patch panel, and then use a spreadsheet if you wish, to know what equipment connects from the patch panel to the switch, or patch panel to the a/v equipment, if you plan on doing HDMI over ethernet. Now of course, there is HDMI over IP networking, but you can only use one transmitter per switch. An example of that equipment can be found at http://www.markertek.com/Home-Theate...I-108POE.xhtml
Also plan on adding in a mix of WiFi for devices on the go, and if you plan on doing Sonos, which means adding in cat-6 for those points. It can add up to quite a few cables once you figure everything out, but keep in mind when doing this, what you may be looking at for future needs. Some will say use conduit or smurf tube, which is a good idea if you plan on hanging a flat panel on a wall, and will be placing equipment nearby, or you plan on hanging a projector, and pulling cables from a cabinet also nearby.