First thing to do go back into your FS9 aircraft folder and open the folder you put in there that contains the aircraft.
If another folder shows up in that folder open it.
Look for the Aircraft.cfg file. if it is in this folder back out one level so you see the folder and not the files it contains.
Rename this folder just add any character to the name and save.
Cut this folder and back out one layer again.
This should put you in the main FS9/aircraft folder.
Paste that folder here.
Delete the other one you just backed out of.
Rename the one back to what it was before if you want to it is not necessary.
Some developers when they pack their folders it ends up having two layers
It would look like this
c:/program files/microsoft games/Flight Simulator 9/Aircraft/P-39/p-39
Well that will not work FS9 will look for the plane in the first P-39 but the files that make up the plane are in the second one.
It should look like this
c:/program files/microsoft games/Flight Simulator 9/Aircraft/P-39
The files in the folder should be aircraft.cfg, {something}.air, sound folder, texture, model folder and maybe some more.
Hope that helps,