I fly with my thumb on the top of the sticks without any problems. You can do it either way, depends on what works best for the individual. What I see Bryris stating is there is a significant differance in the spring tension between his simulator and his transmitter. So, I think he simply needs to make the spring tension on both the same.

However, doesn't the Great Planes G-3 simulator allow the use of your own transmitter, instead of the provided simulator controller? If this is the case, why would you not use your transmitter, so that there will be no differance between the feel of the simulator and actual flying?