Both options can be found in the iTunes preferences advanced tab, and they are enabled by default
Keep iTunes Media Folder Organized
Copy files to iTunes Media Folder when adding to library
1. Both Options OffThis is the best option, then iTunes makes no modifications to your files.
2. Keep iTunes Media Folder Organized enabled onlyJust enabling this option has no effect if you have nothing in your iTunes media folder.
3. Copy files to iTunes Media Folder when adding to library enabled onlyIf the files do not exist in iTunes then if they are matched by SongKong then when they are saved copies are added to iTunes. But note if you make more metadata changes to these files then that will have no effect on the ones in iTunes because now iTunes is interested in the versions it has added. So from now on you should be loading the iTunes media library rather than the original file location.
If you rename these files then they will be seen as new files and added again to iTunes, this could happen if you changed the rename mask or if the first time SongKong only added fingerprints, and second time actually found a match.
4. Both Options EnabledSame problems as above, but additionally if you do load the iTunes Media folder into SongKong and match the songs then iTunes will move and rename the files according the latest metadata. This means that the songs may no longer be where SongKong expects them to be so that trying to use Undo Changes and selecting the last location will fail, you will have to select the original location.
If you still want your songs copied to iTunes media folder and you want songs renamed according to their metadata using the iTunes format you can let SongKong rename the files instead of iTunes by selecting a suitable format in the File naming tab
ConclusionIts always best to be in control, but if you want to continues using these iTunes options at least you aware of the potential problems. If you use create multiple iTunes libraries for different scenerios note that the two options will always be enabled by default for every new library
These problems are also relevant to Jaikoz users.