In the Txer, set the switch to the desired channel. Channel should have 100% travel in both directions ( e.g.~ 1020 - ~ 2020 ppm in a typical Rxer's channel output.
In the PBox, set the selected Txer channel as the PBox's Flight Mode channel.
Program the PBox's flight mode's gain for each FM position. (e.g. 0 gain to FM1 position, ~20% to FM2 position, ~25% to third FM3 position.) Pbox gain settings are typically a lot lower than Cortex's. Then once flying, adjust up FM2 & FM3 from that starting point. (Some folks like to put the 0 gain on FM 2)
Make sure you have Attitude Assist off on all surfaces. You can play with that later. Never use it on the rudder. As you set the PBox up, always double check this before you fly the maiden as sometimes when you change things, you may miss one Attitude Assist setting. You have to check this setting for each surface in each PBox flight mode.