First you have to set up your stick in the game. To do that go to the control menu and select your stick from the pull-down menu at the top either by name, or, if that does not show up, as "generic joystick". Then set your axes and buttons to your preference. This setup will then be saved as "custom.binds" in the folder that Doctor Ace mentioned. You can then make a copy of this file, paste it into the same folder and rename it to say, for example, "HOTAS.binds". At this stage you are more or less set. When you go to the control menu again the will be a "HOTAS" entry in the pull-down menu, which will restore your settings if you should somehow lose them. Remember to do this every time you change something.