If you only have one system, your system is probably either undersized or your home actually calls for two systems.  Many builders install one system in a home to save money, when two systems are needed to keep the upstairs comfortable. 

If your system was sized and installed correctly, you should consider installing a zone system if possible.  A zone system involves putting dampers in the ductwork to redirect airflow to the part of the house that needs it the most at the time.  Sometimes this addition will improve air movement and help make the upper levels more comfortable.