If the bgl works in FS9 you should be able to put it into any active scenery folder. If you have a folder for static objects, that should be fine. Or if you're adding it to another scenery, you should be able to just put it into that scenery's Scenery folder.
Just be sure that you don't have an exclude file that covers the spot where you're trying to place the Stennis living in the same or a higher level scenery folder. If you're adding it to an existing scenery, or very close to an existing scenery, there just might be a troublesome exclude, so if you find one, just make sure your Stennis file goes into a folder that's higher in the stack.
Could the bgl be incompatible in some way with Instant Scenery? I think probably not, since the bgl compiled to begin with, but you never know. Maybe it compiled but not in a way that FS9 can read it. Did you compile it in or for FSX? Is the actual model within the bgl file compatible with FS9? Not everything that works in FSX will work in FS9, and vise versa...