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I've found those slots to be unusable... you can make it so they will battle you, but you can't use one in battle itself, or else it'll freeze. They also all use the same "??" sprite, meaning you can only add one pokemon.
I hate to call Zel wrong in his own game, but
About the stones:
About the flute, I found a blue flute hidden in one of the caves, but I can't remember which one. Whether that'll wake Snorlax, I don't know, since I'm still chillin' in Johto.