The good and bad thing about using your own Tx is you have to copy and program it for each plane you want to fly. You also have to save a different program if you use a different Tx. For example I use my Futaba 6a and 4vf on Fsone. I had to save a different program to each one on the same plane. Some set ups will work on more than one plane with out any changes. But lets say you set up a transmitter program for the Alpa 1 and then try to use it on a P-51, it will not work without editing the program again. What you have to do is "copy" and program a "transmitter" for each plane. You can still use the 6ex or what ever for each plane, you just have to save a different configuration for each plane.

First, select the plane you want to fly and Fsone will load its default "transmitter". On the main menu near the top left there is a link for "transmitter", after clicking on this click "copy" and enter a name for this new "transmiter" configuration. It should be a name that will let you remember that this "transmitter" is set up for this plane. For example, P-51/6ex would let you know that this "transmitter" is configured to fly the P-51 using the Futaba 6ex transmitter.

Next you will click "edit", this will bring up a bunch of "rungs" and "axis" inputs that are essentially all the "channels" and various adjustments for each one.

On the left you will see blocks labeled "Axis 1, Axis 2, etc." If you scroll to the right you can see each "servo" and a schematic that shows you which rung controls each servo. You can move the levers on your tx and actually see if the lever is moving the correct servo. If not, You will have to follow the "rung" back to the left and changes the "Axis" or input from the Tx. For example, my throttle is Axis 3, so I scroll to the right and find the throttle servo, then follow that rung and scroll back to the left and it it shoud say Axis 3. My ailerons are Axis 4, so both aileron servos have to have "axis 4" selected. At the top of the screen there is also a "View A/c" button that will actually let you see the aircraft so you can make sure the controls are going in the right direction. If not, you will have to reverse the input or the output. For instance, if you watch the aircraft and the rudder moves left when you move the stick to the right, then you will have to reverse the control. You can do this for the input by selecting "norm" or "rev" to the right of the "axis" block. You can also do it for the "output" which is just to left of the "servo" display. Either one will change the end result. There are some planes and/or Tx's that require one or the other, but we won't get into that just right now.

All the other "variables" that are displayed across each rung change the rate,gain, range of motion, and other details for each "channel". The only one you need to worry about at first is the "min" and "max" input value located to the right of the "Axis" block. If your flaps, landing gear, etc don't fully extend or retract, you may have to adjust these numbers to get the proper range of motion, but I would calibrate the Tx before I changed these numbers. And I would get all my "axis" and servos programmed before I caliibrate the Tx . Once you have programmed all the "axis" for each servo, you can save your changes and then go back in and edit again if needed. You may or may not need to calibrate, but you can do this at any time.

In case I didn't explain the order clearly,

1. Select plane
2. Copy Transmitter
3 Name the Tx
4. Edit Tx (program axis's and servos)
5. Save
6. Calibrate Tx
7. Edit (change numeric values for min/max input/output etc.)

Hope this helps, feel free to ask for more help or Pm me if you want to.