I wish I knew more about their setting there... The "Is 3D" being checked is almost necessary in the game for the sound to be correct. You cannot set a "stereo" file to that, since it's already "stereo", and hence is already a "Is 3D" simulated file. You'll have a Left Right sound, but no head turning... As I mentioned, it is used to simulate you turning your head about the different locations on the boat. If you use a "stereo" file, you lose the head turning, and if you un-check the "Is 3d", you'll lose it also, and the sound will then be centered and "flat". Think of "Is 3D" being used to fake a "controlled stereo" effect. I could guess, but I don't know exactly how they do it, but it does work, for the most part. They simulate the stereo, and then turn the fields the opposite direction of how you turn your head in the game... There are VST audio plug-ins for programs that I have that do similar.
You could download
Audacity Audio Editor and look at the files in it. It can be a bit of a bother to get set-up and get it fully functional the way you want it, but you should be able to open and look at files without any tweaking. Open Audacity, and do "File... Open..." and "navigate" (dontcha just ~love~ computer talk??) to the Sound folder in your game, and open the "target" file you want to look at. It should display a "wave form" of the file, which when zoomed in on, looks like "wave" lines. It's just a representation of the amplitude at each of the sample points. Anyway, a "mono" file, or single-channel file, will only have one "window" of the wave. A "stereo" file, or two-channel file, will have two of them, a Left and a Right channel. You'll also notice the sample rate listed (44.1kHz, 48kHz, etc), and the bit depth, such as "16-bit PCM" or "24-bit PCM" in various spots in the windows and also in the Properties pages. That PCM just means Pulse Code Modulated, which is the format of the Windows Wave file...
If you set Windows Explorer correctly, you can get it to display the bit-depth and the number of channels used in the file, but for some reason, Windows Update always puts that back anytime it's used... pia...