My wife and I work at home. As a result we have 2 former 'guest' bedrooms that are now offices with heat generating equipment (computers, printers, modems, etc.). These rooms are also at the opposite end of the house from the air handler. Our 2,000 sq ft house now has a 5 ton ac/heat pump (where 4 ton would be normal). The 2 offices each has an extra outlet. The reason is to provide enough cooling so the vents in the offices are open all the way while other vents in the house are partially closed to keep those rooms at the correct temp and force the air to the offices. The problem is when it is cold enough to run the heat the vent openings are all wrong; all the heat goes to the offices that generate heat and the rest of the house is cold. This requires changing the vent openings all through the house when changing from AC to heat (some of them are in 12 foot ceilings!)

Any thoughts on how to better control the air distribution?

The duct situation is not set up correctly. This could be a expensive fix if the duct has to be changed. I would call a qualified contractor and have them look at your situation and get a free estimate at the same time. Always get at least two estimates.