The nice thing about standards is that there are so many of them
You should decide which of the commonly-used channel orders you are going to adopt. For example, Spektrum uses
TAER: 1)
Throttle, 2)
Aileron, 3)
Elevator, 4)
Rudder. Futaba radios default to
AETR: 1)
Aileron, 2)
Elevator, 3)
Throttle, 4)
Rudder.
The consequences of a channel order mismatch between the transmitter (Tx) and receiver (Rx) are obviously bad, and while you could theoretically come up with a custom scheme (TEAR!), I suggest sticking to Spektrum for now - TAER. If you choose to outfit your Taranis with an OrangeRX module, you can then control all manner of Bind-n-Fly models without needing to do wild mental gymnastics to work out which input goes to which channel.
I'll assume that the "sim" model on your Taranis currently has the standard 4 channels - TAER - and nothing else. On the "MIXER" screen you should be able to see CH1 mapper to "Thr", CH2 mapped to "Ail", and so on.
That leaves us needing two more channels for the flaps and wheels. Spektrum convention is to use CH5 for flaps and CH6 for wheels/retracts. There are literally
dozens of ways to configure the Taranis for something like this, but I'll start with something very simple...
Still on that MIXER screen, go down to CH5 and press 'enter'. Give the mix a name if you like, say "flaps", then go to "source" and select "SA". Leave everything else as is, and "exit".
Back on the Taranis MIXER screen, you should now have CH5 mapped to "SA".
Similarly, add a CH6 mix for "SF". (I wouldn't suggest SF for that - those back corner switches are 'panic' triggers best used for "throttle hold" when you come to helis and quads. Consider using say SE instead.)
Now the MIXER screen for your Taranis "sim" model should look like this:
CH1: 100 Thr
CH2: 100 Ail
CH3: 100 Ele
CH4: 100 Rud
CH5: 100 SA
CH6: 100 SF (or whatever)
Over to Phoenix now. Go to the "System" menu, "Your transmitter", and go through the calibration phase once again. This time, you should be able to see Phoenix react to SA and SF when it comes time to calibrate the switches, since the Taranis is now outputting those values on CH5 and CH6 respectively.
After calibration, the last step in Phoenix is to go into "System", "Your controls", "edit" the transmitter profile which I assume you have already created (since you're already flying!), and configure flaps to be activated by "controller channel 5". "Retract gear" should of course be activated by "controller channel 6".
And now if you pick a model with both flaps and retracts, like perhaps the P-47D, SA and SF should have the desired effect
Don't be afraid to experiment and to work out different ways of achieving a particular outcome.