Are you using LaunchPad (yes/no)? It is not necessary to have LaunchPad installed, but it can simplify VDMSound's configuration.
Also, have you installed "Update 1" for VDMSound 2.0.4? If you haven't installed "Update 1" download it from http://vdmsound.sourceforge.net/files/VDMSoun … 0.4.update1.zip and unzip it into the VDMSound installation directory (e.g. "C:\Program Files\VDMSound"), overwriting when prompted.
Now, if you have LaunchPad installed simply "Run with VDMS" (the one with an icon) your game's .EXE. When the wizard pops up simply go to the "Advanced" options/properties, under Joystick, click the button to choose anew mapping file, and select joy3.map (gives you rudder and throttle control).
If you don't have LaucnhPad simply go to the VDMSound directory (e.g. "C:\Program Files\VDMSound"), double-click on VDMS.INI to open it up in Notepad. Scroll down until you reach the "[Joystick Controller.config]" section, and modify the "mapFile" option to say "joy3.map" instead of "joy1.map" (the default).
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