The problem you're probably running into is that there's files in your iTunes folder that aren't in your iTunes Library for whatever reason. You'll have to find an app like Gemini or Araxis FDF to sort through your iTunes media folders for you.
If you're comfortable using the command line; you can use the "mv" (move) command.
mv -n /path/to/source/* /path/to/dest/
The "-n" option tells "mv" not to overwrite an existing files. This should leave you with a merged destination folder, and a source folder with duplicates.
You can then use something like Find Duplicate Files (free for 7 days) to weed out any duplicates in the destination folder.