stiz
With a 1TB drive, just install your entire FSX on it. You won't notice any drop in performance, and FSX prefers it's own HD. I have 4 1TB USB drives now. One each for FSX and FS9 exclusively. The other 2 are for storage of my downloads.
I also load add-on support programs on the drive for the particular FSprogram on the HD for that FS.
To answer your question directly... Yes, it will work fine loading your scenery on a separate USB drive.