There are a few things that can ONLY be changed in the air file. The parameters I've modified in air files are, landing gear drag.. cowl-flap drag, and a few non-performance effecting things like how CHT changes, or fuel pressure, or oil pressure and temperature.
Other than that, as long as the air-file matches the basic model (mainly number and type of engines), everything else can be done in the aircraft.cfg file. In fact, if there's an aircraft.cfg file entry, it overrides the air file anyway.
The key is to use real numbers, and real geometry.. that's 75% of the work. The rest is just fine-tuning.