Copy files to iTunes Media folder when adding to library
This option is enabled by default and if this option is enabled whenever adding songs to the iTunes library it will make a copy of every file and add it to iTunes media folder. So you end up with two copies of every file, one in its original location and one stored in the iTunes media folder.
Why would you want two versions of each file ?
Managing multiple copies of files is an unnecessary headache, maybe there is some concern that iTunes will modify the file in some negative way but it seems unlikely.
If you have this option enabled subsequent modifications to the original file within SongKong will have no effect on the file used by iTunes because iTunes will now be using the copied file in the media folder UNLESS you rename or move the file then iTunes will see it as a different file and add it again !
Keep iTunes Media folder organized
Also enabled by default, this renames files based on their metadata once they are added to iTunes if the copy files options is enabled. But this only renames the copy of the file, it doesn't help you with the original file if it is misnamed. And more importantly you have no say on how your file is renamed, iTunes renaming mask is rather simple and probably not what you really want to use.
If you are using SongKong flexible rename mechanism why would you use iTunes limited filename and you probably don't want to iTunes to rename them differently as they are copied to the iTunes media folder anyway.
And if you are using SongKong to modify files already within the iTunes media folder you certainly dont want iTunes moving and renaming files as they are getting matched ?
Although you can use both options with SongKong I would recommend disabling both.