If there is a spa running in this plumbing there isn't a good spot to put the flow switch to prevent the cell from turning on. The OP will have to do what I do, turn the SWG off while running the spa, he needs to manually turn the valves to select the spa anyways. If they ever get automation, then the automation will control the output percentage while in spa mode.
Good catch Pool Clown for all those who read this for their future setups.