I have a 99 Tahoe it has a rear a/c control when turned on it is cooler than the front i know the front needs to be charged will it effect the rear a/c or not.

 

The front and rear are part of the same system; you can't charge one or the other. However they do have separate evaporators. Poor cooling can be caused by a number of things: Restricted Condenser or discharge hose, restricted receiver/dryer, Expansion valve/orifice tube plugged, Defective compressor (not in your case), System overcharged w/ refrigerant, Defective fan clutch (only at low vehicle speeds).

As you can see it can be a number of possibilities, so before you go putting more refrigerant in the system I would get some manifold gauges to check your head pressures. If you don't know what your doing have a professional check it because you can wind up screwing up your whole system and costing yourself a lot of money.