My daughter has allergy problems. We tried the hepa airfilters that you can move room to room. We found that it took two of them running full time. We tried putting them on timers but it did not seem to works as well. Could believe how much it added to the elctric bill running them full time.
We have since had the duct work cleaned, and use the allergy type funace filters (not the cheap ones) and put a filter on the return air system. You have to change the filters every 30 days, but it makes a huge differnce in the quality of the air in the house. You really have to watch how much you restrict the air movement when you start playing with furnace filters, some are way to restrictive.
I would love to tear out the carpet and put down hardwood floors, but the wife says no.