Lots of guesses required here:
You need to balance your ducts. Close down the ducts where it is warm enough now to give more heat to the far ends.
Many hot air ducts have dampers already installed. Use those. Otherwise, just close the registers in the warmer rooms. http://www.youtube.com/watch?v=mL0mMD_zKaE
Also consider running the fan full time during colder weather to help balance temperatures.