Coming into this a bit late, but I can sympathise with the OP 100%.
I was using a PS3 controller (via cable rather than bluetooth) for ED from shortly after public release. I had become quite natural with it and could land ridiculously smoothly at stations in one gliding movement. Pitch and roll on left thumb, yaw and vertical thrust on right thumb, landing override for lateral thrusters instead of yaw, throttle on lower shoudlers, weapons on upper, plus ancilliaries mapped to all of the other buttons. It felt lacking though as there simply aren't enough buttons to go around - using one of the buttons as a "shift" key was a bit hit-and-miss (quite a few simply wouldn't work for some reason) and power distribution was still on keyboard.
Deciding I could do with more buttons, plus some "muscle feedback" about throttle position (instead of having to constantly look at the bar), and with people raving about HOTAS controllers, I grabbed a TM HOTAS X which arrived last Friday. Got into game that evening expecting to rock the universe, tried out the tutorials first "just in case" and discovered I was utterly crap, to the point that I was wondering why I'd spent the money and was considering going back to the PS3 controller (occasional 3rd-party-driver blue-screens be damned).
I am, however, very glad that I didn't. I have become much more proficient with my new controls (not *quite* as good as I was with the PS3 controller) and I can only assume that the confidence and skill will build further .. it's only been four days play after all (and I didn't get online Monday night). The only time I use the keyboard now is for typing messages and for hitting "ESC" to get the menu up. I have every control I need bound to various buttons (lower button next to the rudder paddle on the throttle is my "shift" key) and everything is feeling really natural.
I'd recommend, if you're not sure what controls you need, use someone else's template as a guide but really go with what feels natural to you - I really couldn't get on with vertical thrusters on the throttle thumb buttons so I've got mine mapped to the rudder paddle (right being up) with the same landing-gear override for lateral thrust instead of yaw (stick twist) as I had with the PS3 controller - I simply don't use the laterals in-flight.
Various combinations of boost, FSD, subsystems, nav panel, sys panel, hardpoints, scoop, shield cells, gear, map, silent running, etc. are all on the throttle controller buttons. Stick is pitch/roll/yaw, primary/secondary fire, target ahead, target hostile (via shift), select fire group (on that handy front-right-side button), pips on the hat, along with menu selection on the hat and select/back buttons on the top buttons. Works really fluidly and I can get to everything I'm currently using, nearly without any thought.
It's a fab controller, loads of buttons, the minor deadzone on the stick isn't an issue once you get used to it and it's definitely the right way to fly. All I need now is to get an EDTracker for looking around (head look via the stick just feels "odd") and I'll be very very happy
Cheers,
QQ