Hi, nothing has changed with Save and Move I think there maybe a slight misunderstanding on your part here. Jaikoz splits each filepath into three components, Base Folder, Sub Folders and Filename.

The Save and Move simply changes the Base Folder to a different Folder, nothing else changes. So in your case it sounds like maybe the files were in a folder such as C:\Music\Rips and SongKong has split the file path into Base Folder=C:\Music and SubFolders=Rips. So if your you set new folder to C:\Music\Final then the files would get moved to C:\Music\Final\Rips
Sub Folders underneath this would be the same as they were before, so if the songs were already organized by Artist/Album then your would still have these folder, if not they would not be created.
So it sounds like you need to modify the split between Base Folder and Sub Folder. The split between Base Folder and Sub Folder can be modifified with the Shift Base Folder to Sub Folder and Shift Sub Folder to Base Folder options
If you don’t currently have Artist and Album subfolders then you need to run Correct SubFolders from Metadata as well.