This was my sons reply last night.
As an example here is my complete controller section from my xca (pretty much default cfs3). Note the 'Axis ID="Throttle"' section for both controllers are bound to different actions. The game differentiates between the axes for ch flight sim yoke vs ch pro pedals because they are subsets of different devices.
<Device Type="CH FLIGHT SIM YOKE USB">
<GameMode Name="Player">
<Axis ID="X" Action="Set_Bank" Scale="64" Nullzone="36"/>
<Axis ID="Y" Action="Set_Pitch" Scale="64" Nullzone="36"/>
<Axis ID="Throttle" Action="AXIS_THROTTLE_SET" Scale="127" Nullzone="1"/>
<Button ID="1" Action="Fire_Guns"/>
<Button ID="2" Action="FireCannonsOnly"/>
<Button ID="3" Action="ReleaseFireWeapon"/>
<Button ID="4" Action="SelectNextWeapon"/>
<Button ID="5" Action="FLAPS_INCR"/>
<Button ID="6" Action="FLAPS_DECR"/>
<Button ID="7" Action="NextTarget"/>
<Pov ID="1" Action="HeadPov"/>
<Button ID="8" Action="TogglePadlock"/>
</GameMode>
<GameMode Name="M3DViewer">
<Pov ID="1" Action="HeadPov"/>
<Button ID="3" Action="ZoomIn" RepCnt="1"/>
<Button ID="4" Action="ZoomOut" RepCnt="1"/>
</GameMode>
<GameMode Name="Gunner">
<Axis ID="X" Action="TraverseGun" Scale="64" Nullzone="36"/>
<Axis ID="Y" Action="ElevateGun" Scale="64" Nullzone="36"/>
</GameMode>
</Device>
<Device Type="CH PRO PEDALS USB">
<GameMode Name="Player">
<Axis ID="X" Action="AXIS_LEFT_BRAKE_SET" Scale="65472" Nullzone="36"/>
<Axis ID="Y" Action="AXIS_RIGHT_BRAKE_SET" Scale="65472" Nullzone="36"/>
<Axis ID="Throttle" Action="Set_Yaw"/>
</GameMode>
</Device>