Your application and your Police Certificates should match, ideally. But, a police certificate in Pakistan is issued on CNIC. So, if you have a CNIC issued from AJK, you must get a PCC from there. Most probably that PCC will be sufficient, as that will cover your stay in Islamabad as well as Lahore. If you try to get a PCC from Lahore, they will first ask you to get an ID card issued from Lahore, then they will give you a PCC.
When I applied for Immigration, I used to live in Rawalpindi, so, I got a PCC from Rawalpindi. After that, I shifted to Lahore. Again, there was a need to submit my PCC, so I got that from Lahore. But, in getting my PCC from Lahore, I showed them that I already had a PCC from Rawalpindi till, lets say, September 2014 and told them that I need the next PCC from October 2014 till date, and they cooperated. Its their headache to ask Rawalpindi Police whether this person had any criminal record there or not.
In my opinion, when a person commits a crime, his data is updated at NADRA. Therefore, it might not matter from whichever city of Pakistan you get your PCC.