The S3 is a new product and you are the first I have seen have it so I am just working off the manual.
The manual says the following:
Features
The AquaRite S3 offers the following features:
• can generate chlorine using a broad range of salt concentrations from 1200 PPM to 8000 PPM
• can control and schedule a Hayward Variable Speed (VSP) pump using the internal RS-485
connection, a Pentair VSP using a Hayward HLPMPCONV converter (sold separately) or a single
speed pump using a Hayward Smart Relay (sold separately)
• can control a gas heater, heat pump or any other heater that uses a low voltage on/off remote
connection (requires Hayward water temperature sensor sold separately)
• inputs for water and air temperature sensors (temperature sensors sold separately)
• connection for flow switch used to detect water flow
• connection for pool cover detection (lowers chlorine production when the pool is covered)
• can be powered by either 115 or 230 VAC
• offers recirculation freeze control which turns on the filter pump automatically to prevent freezing
(requires Hayward air temperature sensor sold separately)
If you have that box then you should have all those features.
The pump just needs to have power for the automation to see it. It does not need to be on and have flow.
Page 13 in the S3 manual says:
Hayward Variable Speed Pump (VSP) Wiring
The Hayward TriStar 950, TriStar 900, Super Pump 700 and MaxFlo 500 pumps wire directly to the
RS-485 connector and will be fully controlled by the AquaRite S3 (schedules and speeds). Refer to
the VSP Communication Wiring table and diagrams on the following page for VSP communication
wiring instructions. For Pentair VSP models, use a Hayward HLPMPCONV converter (sold separately).
Refer to the HLPMPCONV instructions for wiring information. After wiring, run the communication
cable through the low voltage Wiring Channel (same as Smart Relay above).
Your problem may be that you do not have a Hayward TriStar 950, TriStar 900, Super Pump 700 or MaxFlo 500 pumps that wires directly to the RS-485 connector and will be fully controlled by the AquaRite S3 (schedules and speeds).
I suggest you call Hayward Support and see if the Superpump VS you have is compatible with the S3.
It would be a shame for your builder to have given you a pump that is not compatible.
I would demand the pump be changed to a compatible pump the S3 can control.