Still, if your tap has 2 ppm of ammonia and you have 4 ppm total, then your tank isn't cycled or you had something happen in your tank that is to blame for the excess ammonia. This could be overfeeding, dead fish/plants, a sudden shift to an alkaline pH, etc.
Doing a 45g PWC on a 90g tank with 4 ppm ammonia to start with will give you 2 ppm of ammonia assuming that you add ammonia free water. Since you are adding 2 ppm back into the tank you will be looking at an ammonia reading of 3 ppm. The lowest you could go with your tap water at 2 ppm would be 2 ppm. Might as well not even bother with the PWC in my opinion. I'd just add extra Prime or some other water conditioner than neutralizes ammonia. You are going to have to do this every 24 hours since that is how long the effects of Prime last roughly.