The proper way to size an air conditioner or heat pump is to have a computerized heat load done as well as a duct inspection. This will give you the proper size unit for the most efficiency and longest life!
Yes, the unit can only reach it's efficiency if the duct system can deliver the air to the home. Undersized ductwork puts a strain on the unit that will shorten the compressor life, cause the unit to overflow the condensate drain and damage drywall, and cost you more to operate. In testing throughout the US the average unit delivers only 65% of the units airflow due to inadequate ducts, costing homeowners thousands of dollars per year in wasted energy!
Yes, using better filters will allow the unit to stay cleaner allowing it to maintain it's efficiency saving you money, as well as improve indoor air quality making you feel better and make your furnishings last longer.