Like you I just moved into a brand new home with structured wiring. I have Cat5e installed throughout the entire house and I was excited...however, my excitement soon dissipated. See, those CAT5e ports in all your rooms default to phone jacks. So that means you have to choose between phone or data. You can't do both because you run into funky voltage problems. You don't want the phone to ring when you have the jack connected to your NIC...you could fry your hardware since the phone line sends like 90V when the phone rings.
In order to change all or some of them to data, you'll have to use the second set of wires. To my disappointment, all the data cables were non-crimped. I don't really know a whole lot about crimping patch cable, but I know it's a lot of work. So I just went wireless. However, you can have the structured wiring folks come out and convert it for you. I just wished that they had phone and data connected. I mean, under the little panel, you have Cable, phone and data right there at your finger tips. Theoretically you can connect your Cable Modem, router and switches all in the closet and just plug your PC into a wall jack. However, it will take a little work to get it running. But you're right, your house is wired for data, phone and cable. The coolest thing I noticed is how the Cat5e ports allow phone cables to be easily plugged into them.