I recently removed my stock shifter 5 speed manual in my 2005 cavalier and I forgot to mark shifter cables were there were hooked at in clips at shifter assembly. It is now kind of rough getting car into various gears. How do I readjust cables at shifter so shifter works smoothly again?

Assuming you installed a different shifter, I would recommend the following. Place the car in neutral. You can verify neutral by seeing that the car rolls easily with the emergency brake off. Then release the two shift cables. Position the shifter as close to center as possible. The side-to-side position will be determined by the shifter itself which is spring loaded to place the shifter in the center neutral side/side position. Lock the side/side cable. Then with the shifter still centered in the fore/aft direction, lock down the fore/aft cable. Then test the shifter for proper operation. Some slight readjustments might be necessary to recenter the shift pattern, but you should be good to go.