This is usually just a matter of balancing. Meaning adjusting the airflow to each room so they all even out. Or sometimes making the rooms you want comfortable and unused rooms less so. If a room is heating or cooling much quicker than other rooms, the air-flow can be lowered to that room to even things out, also sending more air to other areas.
If some rooms can't keep up with others and the airflow isn't as noticeable, make sure the vents are fully opened.
What is the best way to balance? Many systems have dampers installed on the individual supply runs coming off the main supply trunk. This is either in the basement or attic. They are identified by little metal handles which open, close and adjust a metal damper controlling the amount of air through the duct. By dampening the air-flow here to rooms with too much air, it will send more air to the rooms that need it.
If your system doesn't have dampers or if they are inaccessible, then dampening and balancing will have to be done at the supply registers themselves. Just adjust as necessary.
In most homes, mostly two-story homes, there is always one or two rooms that just can't keep up with the others. Maybe it has the longest duct run with the most elbows and turns. Maybe it is over a garage with more heat loss or isn't insulated as well. Whatever the case, balancing should help.
Below is a list of possible causes and things to check.