I haven't got mine yet, but wouldn't it make sense to have the pitch and roll on the Y and X axis of the yoke, the Yaw on yoke-twist (instead of rudder pedals) and then have the thrust up/down/left/right on one of the hat switches on the throttle?
Would also be very interested to hear how those with the X55 currently have it set up!
At the moment I've got the lateral & vertical thrusters set up on one of the hat switches on the stick. However that's not really what I want. Ideally it should be one of the hat switches on the throttle (as you suggest) but the last time I tried to set that up, none of them were recognized by Elite Dangerous.