Scanning multiple libraries

Currently I have SBS scan my iTunes library (by checking use iTunes).

But I'm in the process of re-ripping important suff to FLAC outside iTunes. Can I have SBS scan both iTunes and FLAC Libraries? I have seen references I think it was in the manual to SBS can only scan one folder (and sub-folders). is there a work around?

Does the scan work from the iTunes index, or from scanning the iTunes music folder?

Also will the scan of a non itunes folder follow shortcuts? Would one approach be to put a shortcut to the iTunes music folder in the FLAC folder?