Moved to the Audio forum from the Living Room.
Providing that is a legal download some FLAC files already have the cue embedded on the file itself.
Foobar2000 is able to open correctly these files. If the CUE is embedded, loading the FLAC on foobar will show you all the tracks.
If not, I think that you can open the FLAC with an audio editor like Audacity, and split manually tracks (I never did such a thing, so I have no idea if it will work, but you can give it a try)