I was in this same situation. I got a RTF Alpha trainer which came with the JR S400 radio. I then built a Sig Four Star, and set it up identically to the Alpha, so I could use the same radio. When it came time to buy the flight pack, it was only about $9 more for the whole radio including TX, so I ordered an additional S400 system on the same channel.

Now I had two identical radios, for which I mechanically set up both planes to be identical. Then, I finally got my AMA buddy box in the mail, and set that up to match as well.

Then the problems start. It turns out that my RTF Alpha trainer was set up funny at the factory. I had to reverse the throttle channel when I got it, as well as the elevator (I think). Now I have two planes set up this way. Then, I decided to set up my Slow Stick to use the same radio. As you can guess, with an electric plane, you have to keep the throttle in the original, non-reversed position. So I have one of my identical radios now set up for the Slow Stick, and the other plus the buddy box set up for the glow planes.

As you can see, it can become a confusing mess. I would second the recommendation to go with the 6 Channel JR computer radio for $160. It will save a lot of headaches, and could possibly save a plane if you ever ended up switching radios by accident.