If you are able to move the four dots representing the axis movement of both sticks smoothly up and down you should be fine.
Keep and eye on the dots as you go through the calibration. They should turn into "thr/yaw/pit/roll" respectively as you go through calibration. That way you can tell if the correct stick gets assigned to each channel.
If the automatic stick detection gets it wrong, you can manually click on the dot that you see is the correct one for each stick (instead of clicking "OK")
(You still need to hold the stick fully in the direction shown for the calibration to work properly)
On the Trim Settings screen you have the opportunity to trim/scale/invert if necessary.