[itsme]

I think I would have a separate file per tune and import every file as a song.
Then create a copy of the first song of a pair, add the second tune and save it as a new MSP song under a new name like "first tune + second tune"
Tune-songs and tune-pair-songs can easily be grouped in collections, setlists, albums, custom groups, whatever fits best. I use collections for bands / line-ups / session locations and MSPs setlists to plan the programs for gigs.
With MSPs search function it's easy to find every song and every pair that contains a certain tune.