Don't go by colors of CC3D wires because some clones use different colors. Go by the pin number of the CC3D connector. They aren't actually important anyway because when you run the wizard, it sees which wire you are using for roll, etc. and automatically uses that channel for roll, etc.
You must start with a good transmitter wizard run. You must follow all directions.
Assume that anything you skip or don't understand is the problem.
Modern transmitters usually require you to configure any switch that you actually want to use. If you don't have a Flight Mode Switch channel configured on your transmitter and plugged in from receiver to CC3D, it won't see an FMS. If it doesn't see an FMS, there is a display issue in GCS setup where it does not show the sticks / switches / sliders moving in the transmitter wizard after a certain part. After getting all that working, you will be able to set the control directions correctly on the wizard page that does that.
I thought I had it sussed this morning but when flying for the first time, some of the controls were wrong...
Some of the controls move opposite when looking at the controls on the laptop. And when flying they aren’t doing as I’m asking.
Wrong how? Reverse direction?
Flight data page PFD roll may seem backwards but isn't, When you hand move roll the quad left, the world that you see through the PFD rolls rightward.