I have started a project to embed my FLAC files with the cue & artwork.
Why?
MC12 does not support embedded cue sheets.
As a workaround, you could keep the external cue files until the track details are imported to the library. MC does not use the cue files after the virtual tracks are created.
Personally, I don't undestand how a small cue file inside the file folder would make things untidy.
In general, standard separate track files would be a more compatible way to store audio CDs. MC's Library Server and most HW devices do not support the disc image + cue format.
I store my archived rips in an album image + cue format on backup drives, but in my MC library I use converted track files.
Only those rare CDs that have a hidden track before the track one (in the pregap) actually need the album image format if there is a need to recreate the complete CD (in this case EAC or CDRWin is needed for burning the image). To play such a track on a PC it must be separated manually (e.g. by creating a custom cue sheet and converting the first track to a separate file).