Most of this data is in the User Manual (located in your BOBII folder in the Docs folder) with Pic's but maybe this will help you. Sorry, I do not have or understand your joystick as I am a CH (CH FighterStick and CH Pro Pedals) player.
Go to CONTROLLERS->CUSTOM NOTE: Be sure your joystick is selected in the pull down list.
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 recognised.
1)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.
2)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.
3)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.
Her is a pic of my CH assignments:
4)Goe back to controllers, then click on KEYMAPPING.
5)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 in the lower left corner or your keys will not be saved.