Here's how I do it, and I just finished an office like this a few weeks ago. I wish I took some pictures.
1. Run all CAT5 or 6 cable from a central demarc (where your router, switch, etc go), to each office/bedroom/desk - anyplace you want a wall jack for phone or internet.
2. Wire all the runs at the demarc into a standard data patch panel
using 568B wiring scheme - that's your "hub", so to speak. You connect a patch cable for any data connections from the patch panel to a network switch.
3. At the wall plates in each room, I install a blue CAT5 keystone jack for internet access (wired for 568B) and a white RJ11/RJ12 keystone jack for copper/POTS telephone. (You don't use CAT5 jacks for telephones, regardless of what some cookie cutter tells you on the internet). Using the correct jack also prevents you from sending 50 volts to a network device when the phone rings because someone mistakenly plugged a computer into a telephone line.
You can buy standard data wall plates that will accept 1 to 6 keystone jacks, so no need for any special combo jacks.
- At the wall plate, take the CAT5 run you want to use for phone and wire the RJ11/RJ12 phone jack using the blue pair of wires for line 1 and the orange pair of wires for line 2 (if you have 2 telephone lines w/a 2 line phone). Leave a foot or more of extra length of cable in the wall for future use.
Blue wire = pin 3 on RJ11 jack (-)
White/Blue wire = pin 4 on RJ11 jack (+)
Orange wire = pin 5 (-)
White/Orange = pin 2 (+)
Use this info when wiring the RJ11 phone jack and when connecting to the phone block your telco. provides.
5. Make a patch cable with an RJ45 jack on only one end and leave the other end with a few inches of the jacket removed, so your 4 pairs are exposed. Plug the RJ45 end of the cable into your patch panel for your phone line. Now you can use the blue pair of the exposed wires to connect directly to the telephone block the phone company provides. Repeat this step for each "telephone" line that comes into your patch panel.
If you wire it this way, all you need to do is cut off the RJ11 phone jack at the wall plate and replace it with a CAT5 jack and you now have a data run for an IP phone. Just remove the patch cable you made in step 5. Wiring everything to 568B at the patch panel means you never have to re-punch anything and risk disturbing the existing wiring.