Take your Nikah Nama to the marriage rigstrar (would be The Respectable Molvi Sahab of the Jamiah Masjid of your UC or area) and he will make a C Form for you. That is a simple paper with your details of nikah typed in Urdu and English (your and wife's name and NIC numbers, you and your wife's FATHER's Name and NIC numbers ... details of Haq Meher and Name and NIC of the Nikah Issuer (Movlie sahab who read you your rights and bonded you and your wife in holy matrimony AKA Life Sentence!)
With these particulars filled he will stamp it for you.
Take that C Form now and take along copies of your, Wife's, Father's, Father in Law's and the Nikkah Issuer NIC's plus a copy of your original Nikah nama to the Union Council OR Cantonment Board depending upon the location where you held and registered your Nikah
The fee is normally around 240 to 300 plus may be some Tea/Biscuit allowance of the guy who makes that Marriage Certificate.
They will ask you to come may be in the evening or the next day to check the details and spellings on the form and take home the finalized Marriage Certificate
I hope I helped You are lucky I am a few days ahead of you in getting my wife's ID change done and been through a hell lot of places to finally understand the bits and pieces required to get it done
One guy even asked me to give him my passport and PKR 10,000 and he will get it made for me in two days
Your wife does not need to go any where in the process or no signatures are required. This basically is the job of the Marriage Registrar to have this done for you ... BUT ...............