Here is a link to the Comfort Alert Manual, It will explain the operation better than I can do by copying and pasting the info which will violates our terms of service but I can give you the link, and you can read the copyrighted information.
We are only concerned with the expansion valves that are on the indoor coils, They need to have a pressure relief bleed port. Keep in mind that Scroll compressors are louder when they shut down than the same capacity reciprocating compressor.
To ensure that the machines are functioning in a 2 stage operation, all you need do is listen to the indoor units. and at both stages check the temperature drop between the supply air and the return air. And be sure the drop stays about the same between stages, even though it is moving more CFM.
As far as heating the furnace control board has a setting that has a timer if 1st stage stays on for 5,10, 15 minutes depending on setting the second stage of heat kicks on both the burner and the blower will pick up speed.
In the installation and operation manual there are tables that tell how to set the dip switches on the control board for low fire heat, high fire heat, low cool, high cool.
You'll be given choices on blower profiles and on and off times, as far as comfort or economy, the system is very economical naturally when you have variable speed systems they are built for comfort. You'll have to decide if you want more Dehumidification, or sensible cooling.
Blower choices will be 350 cfm per ton, 400 cfm per ton, or 450cfm per ton.
I have to assume that your installer knows how to set the blower speeds, by the way the table is also on the blower door.