Good deal,
First open the program and drag the prop texture onto it. you will then see this:
See the white square area in the top right corner, that's the alpha channel, for transparency in FSX the darker it is, the more transparent it is, in FS9 it was the opposite, since it is currently white, all of the black area on the prop texture shows in game.
Now from the drop down menu at the top select alpha channel, and then select invert alpha and you should see this:
The white square area has now turned to black, so when it loads in FSX now, all the black areas on the texture will be transparent.
Finally go to the file menu and select save, and you are done.
This same process applies to blackend out windows and glass textures in FSX.
Since there are three different texture folders with this plane, you can either copy the one you just fixed into the other two, or fix them in the same manner, your choice.
Good luck and let me know if you need anymore help with it.