A couple of years ago we had an American Standard system installed to replace the existing unit. It had the variable speed fan also, much like your system. One thing to check though, is whether the compressor is a 2 stage compressor. The system we put in was a 2 stage compressor and had to have a compatible thermostat. Installer had to go get one and said the regular one would not work correctly. Good luck to you and relax a little. They will get it figured out and you paid them a lot of money for a system that works correctly, don't settle for less.