Start with a new default Acro model on your DX6. This is Mode 2 with the stock mapping of channels for a plane in standard configuration and ensures that the radio isn‘t remapping the controls.
If you have changed any settings in the Windows Game Controller Setup for the dongle, reset it back to default.
Open the Select Controller... dialog in RF, select the dongle and Edit it. Reset it to defaults and check the mapping.
If the mapping is not correct at this point, click on the Input box on the right end of any Channel that isn’t mapped correct, them move the correct control/direction. RF will see the moves control and map it to the channel. If it is the correct control/axis, select or unselect the Reverse checkbox until it is correct.
Mode 2 is the default input expected by RF, so be sure that you have the Functions on the left side as:
Channel 1: Ailerons: Right Stick X-Axis
Channel 2: Elevator: Right Stick Y-Axis
Channel 3: Throttle: Left Stick Y-Axis
Channel 4: Rudder: Left Stick X-Axis
When it acts like you expect or want, save the setup then calibrate it. You should be good to go.
I don't quite understand the confusion. This setup procedure is covered quite well in the on-line manual ... under "HELP". Sort of sounds like you are trying to calibrate without first setting up the controller. Try hitting edit before you calibrate and follow the instructions. There are "check boxes" for reversing each channel. Reference the manual for specific details. Starting a new thread just gets the same responders in most cases.
It's also possible that the OP is editing the setup using the Windows Controller Setup interface, rather than the Select Controller dialog in RF. Dunno. I just cut and pasted the response from my growing library of FAQ's, so it took longer to type the question than for me to provide the answer.