I have run Cat 6 throughout my house as opportunities arose (mostly while working on other areas or remodeling rooms and could open up walls). I purchased my box of Cat 6 from monoprice.com, as well as a bunch of keystone jacks. Most of the bulk quantity bags of those include a tool (simple, but usually does the job) to press the wires in place in the jack and the color coding is pretty standard. Just make sure they are all the same (A or B, choose only one) connection method.
When running the cable itself make sure not to bend it TOO tight (kinking it) or punching a staple through it. Those can be good ways to sheet a wire (they are pretty thin) and making that whole run worthless unless you can find exactly where you damaged and salvage the other parts. If you can borrow one or buy one, I recommend a network jack tester. Usually <$20. Before everything is closed up and there is still opportunity to replace a damaged cable, test the cable and make sure it works. If you do not have a tester you could always use a simple network device but that takes longer and does not test EVERY wire, important if you ever think you might need PoE or possibly future standards.
Having everything run from one place where you will have your main network area is very useful BUT you want to plan it out a bit. Our house is a split level and I could have saved a lot of wire (and effort) if I had just run a couple wires (I generally try for two per plate at least, better to have extra) to the other section of the house and put a small panel and switch in there ALSO rather than running long lengths for every single connection. Unmanaged switches are pretty cheap and you can get enterprise grade ones (although older models) on ebay readily, even managed ones that are overkill for a home.
I also mentioned it before, but better to run extra. If you ever decide you need an extra port somewhere and did not run the wire while you had the opportunity it can be a real pain to rework (if at all possible). So I always recommend planning it out a fair bit and then including extras to each major area. Other than the possible connectors and wire expense it is relatively cheap and easier to do at one time. If you want to save a bit of cost on connectors you can always run the wire but not put jacks on them... although that makes them tougher to test.
For wherever you will have all the wires terminate, get a patch panel. It makes it a lot easier to organize them all. I even have COAX coming to mine from a couple spots, again just to keep it all simple. I also mentioned using Keystone jacks. There are other options out there but I have found those to be generally reliable and they come in a variety of colors (can help make it easier to figure out which cable runs where) plus you can readily mix & match the actual wall plates readily for different options or other connectors.
Let's see... if possible, consider OTHER wiring you might want to install at the same time. Speaker wires, coax runs, stuff like that. Again, easier to do it at one time.
Last thing I can think of, if you DO need more than a single 1000ft box of Cat 6 (or 7), get two different colors. This (like the jack colors) can make it easier to figure out what is going where. It would have made my life easier at times.
I am probably forgetting stuff, but feel free to ask more questions.
