There are a few different considerations you'll need to take into account when taking on this project:
1. You need to check with Avaya... I am particularly concerned with the age of the system - I believe many years ago, Ayava systems used 1 pair digital (for signalling) and 1 pair analog (for actual voice). You'll need to get in touch with your phone system vendor and ask them what the wiring pin-outs are for the station ports; this is what will dictate how your voice wiring will go.
2. Cat6 can be used for anything, voice/data - simply Cat6 has higher shielding and tighter twists of the cable, eliminating cross talk and giving higher throughput - voice is extremely forgiving and non-voip doesn't even require twisted pair.
3. I'd seriously re-visit your phone system - upgrading your system (while expensive) may be a CapEx cost that is viable, seeing as it will bring down the wiring cost (so you won't have to install dedicated voice and dedicated data). Structured wiring CAN be expensive - upgrading a phone system might/might not fit the budget, but it WILL be advantageous going forward.
4. Again, if you upgrade your phone system, you're not going to need much in your telco/server room except data terminations. Obviously your GC should be putting in a 3/4" backboard with #10 dedicated ground (pretty standard). Also your ILEC will want a conduit to the minimum point of entry (MPOE) to drag copper/fiber. I'd STRONGLY advise (if possible) to install two 3-4" conduits to the MPOE... Typically ILEC's will try to drag copper in (because it's what their used to doing and still [sadly, to this day] required for FACP/Alarm lines/Elevator lines).... Most ILECs *WILL NOT* pull fiber into an existing conduit (unless there's innerduct separating copper/fiber -- and it's a HUGE pain to install post-construction).... If you CAN manage, get a second conduit to the MPOE so when they offer fiber they won't complain about there being no conduit.
5. ALWAYS, ALWAYS, ALWAYS over-build your physical network during construction... If you think you'll need 48 ports, double it - trust me, you'll understand in a few years.
Enjoy - this should give you a really good start on your project - let me know if you have any questions.--