You have this wrong, what you need to do is think
BIG!
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I use TWO Logitech Extreme 3D pros! The reason for this is that throttle control IMHO in this game is secondary to thruster control. Once you enter a RES site etc. simply set the throttle in the middle of the blue and in combat control your forward/back speed with the thrusters. You only need to use the throttle when running or chasing. So on the right hand I have pitch/roll/yaw and on the left hand thrust forward-back/left-right/up-down. Full loadouts as below and instructions for setting them in the order they appear in the controls screen. POV is the hat. The OFF/ON refer to reversing the axis.
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With this setup I never have to take my hands off the joysticks except to set the power pips and I do that via pre setup macro keys on a Logitech G110 keyboard so it's 1 key push to change settings. I would recommend having forward and back on the throttle as it makes rapidly reversing out of the docking slot much easier when you realise you have forgotten to ask for docking permission.

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Left Joystick
Lateral thrust: X axis pull right OFF
Vertical thrust: RZ axis twist right OFF
Forward/back thrust: Y axis push forward ON
Speed to 50% joy 7
Cycle next ship: POV up
Cycle previous ship: POV down
Cycle next hostile target: POV right
Cycle previous hostile target: POV left
Target next system in route: joy 8
Secondary fire: joy 1
Deploy hardpoints: joy 6
Ship Lights: joy 9
Cargo Scoop: joy 10
Landing gear: joy 5
Use shield cell: joy 4
Use chaff launcher: joy 3
Open galaxy map: joy 11
UI panel focus: POV down/right
UI target panel: POV up/left
UI system panel: POV up/right
UI system sensors: POV down/left
UI panel up: POV up
UI panel down: POV down
UI panel left: POV left
UI panel right: POV right
UI panel select: joy 2
UI panel tab next: joy 4
UI panel tab previous: joy 3
Galaxy map translate Y axis: Y axis push forward ON
Galaxy map translate X axis: X axis pull right OFF
Galaxy map translate Z axis: RZ axis twist right OFF
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Right Joystick
Flight rotation yaw axis: RX axis twist right OFF
Flight rotation roll axis: X axis pull right OFF
Flight rotation pitch axis: Y axis pull back ON
Throttle axis: U axis push forward ON
Speed to zero: joy 11
Speed to 75% joy 10
Disable flight assist: joy 5 toggle
Engine boost: joy 3
Enable frame shift drive: joy 12
Enable FSD to supercruise: joy 7
Enable FSD to hyperspace jump: joy 8
Select target ahead: joy 4
Cycle next subsystem: POV up
Cycle previous subsystem: POV down
Primary fire: joy 1
Cycle next fire group: POV right
Cycle previous fire group: POV left
Silent running: joy 9
Deploy heat sink: joy 6
Galaxy map pitch axis: Y axis push forward ON
Galaxy map yaw axis: RX axis twist left ON
Galaxy map zoom axis: X axis pull left ON