Welcome to BOBII. I assume you have the CH throttle working in game (axis assigned correctly but if not see step #1-#5) and the issue is the assigning buttons.
Try these steps to assign the buttons (step #6 abd #7):
1) Before you start trying to configure your stick in game, make sure all switches are OFF.
2) CONTROLLERS, CUSTOM
This is where you can assign the main joystick axis.
Left click on the required axis under the "assign axis" list. The axis should be highlighted red. The move the required axis in it's full range of motion and it should be recognized.
3)If you make a mistake with the axis assignment, highlight the one you want to undo then click on "clear" to return to it's default setting.
4)Repeat until all main axis have been assigned to your liking.
Once complete, click on CONTINUE (top right of screen). And when asked if you want your changes saved, click on YES.
5)IMPORTANT. Now, exit the game back to desktop, then restart it. The game does not permanently keep any changes or settings unless it has been quit & restarted (CTD does not count).
6)Go back to controllers, then click on KEYMAPPING.
7)Scroll through the list, and left click with the mouse once to highlight the current button/key assign to the control of your choice. At the bottom, a message will appear:
"polling input devices.. please press the button you want to map, or the "cancel" button to stop polling. Press "clear" button to remove a mapping."
When you press the required stick button or key, this should be recognised and listed by the function you wanted to remap.
Repeat for all commands required.
NOTE: You must hit "save" on the bottom left of the screen to save the joystick keys. If you leave without hitting save the keys will "not" be saved.
You might also want to look at and download our "key description" document which can help you understand BOBII keys:
http://shockwaveproductions.com/forum/v ... php?t=8331