yaw, collective, flightmode, etc are all just convenient names that are attached to channel numbers. this is a simplification, but for this issue you can think of it this way. it's more correct to say that e.g. the yaw value comes from a formula that uses the value from an RC channel number (stick position) where you select the channel number in the transmitter wizard.
to put flight mode on accessory 0 you move type, number, min, neutral, max of the accessory 0 line to the flight mode switch line. make sure you don't have any duplicate channel numbers though, unless that is your intent, like putting throttle and collective on the same channel number.
for channels that don't work, realize that if it doesn't show in the activity box, that CC3D can't see it at all and you must do some radio configuration. Radio switches and sliders are often this way. You must configure them in the radio for CC3D to even be able to see them.
I would suggest that you first get all channels that you need showing in activity box, then re-run transmitter setup wizard and during wizard be careful to include all sticks, switches, sliders, pots that you need. When done with this, take a screen shot for your future reference. Then you can swap say accessory 0 with flight mode switch by swapping all the values on the accessory 0 line with all the values on the flight mode switch line.