It's a while since I did it, but IIRC the things that you need to do are:
In your transmitter, make a new ,model. Set the protocol to PPM;
In Phoenix, use the transmitter profile wizard;
After that all transmitter settings are done in Phoenix, like servo reversing for controls that work backwards.
Solved. I'm going to recap a bit and go into a little detail, for the next guy.
The trans kept losing my settings for everything. Including PPM. I finally figured out that was because during my troubleshooting process I kept changing the model type between helicopter which is what the Phoenix manual said it to had be and airplane because that's what I was trying to fly.
With the Turnigy, when you change the model type it basically erases everything else you set up. Once I had that little epiphany, I stopped having the problem of losing my settings, and the sim not recognizing my trans. I left the model type on airplane. Installing the directx 9 driver was also essential.
I was then able to go to the next step you suggested: "After that all transmitter settings are done in Phoenix, like servo reversing for controls that work backwards."
It took a little while to figure out, just because I really don't know what's supposed to do what. I unmapped everything that was helicopter and through some trial and error manually set the channels to get stuff to work. I still can't get my landing gear switch to work, and for some reason my throttle stick is activating both channels 3 and 6. Also not a big deal at the moment, since I'm not utilizing channel 6 for anything.
All that being said, I am now flying a plane in a sim!
Thank you for your input, d8veh. Couldn't have done it without you.
Getting the FT models in was a whole other challenge. I'm going to start a new thread for that one.