Glad to be of help.
I looked a bit deeper into it and it appears the Enviolo Cliq CO controller is used just for set up without the phone and its app. I find no information about using it to shift while in manual, 9 speed mode. It appears that manual is available only using the phone app. To enter manual mode, go to the app dashboard and touch the little round button with the A in the middle at the upper left of the screen. It should switch from A to M indicating you are in manual mode. Then the big arrows in the middle of the screen can be used to shift up or down. All this presumes that your phone app and the hub are connected. If you want to actually shift manually, you will need to mount a secure phone holder like a Quadlock, close to your right grip so you can shift conveniently.
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Clearly Enviolo does not want people who have the Automatiq to be using a thumb operated shifter in manual mode. Fortunately after riding the bike in Auto shift mode, I see no need to even use it manually. It is uncannily good at shifting to the proper ratio for the terrain. I am even thinking about taking the Cliq Co controller off the handlebars and just leaving it at home as I never use it either in setup or while riding.