Premising I haven't read the manga after the Red saga, and even that was a long time ago, I scrambled some informations thru Bulbapedia and Google, so I'm positive about my answer.
Put shortly: No, it was never canonically explained how they met.
However due to Emerald's kind and loving nature towards Pokémons, even if he didn't realise/ admitted it until the final fight against Guile, one could speculate that, based on their behavior in the movie in which they appeared, they appreciated and shared his inner feelings, thus mentoring and looking over him until, as evidenced by their departure, he met new friends.
it could just be a plot necessity, like "Hey, this new character needs something cool…
HOW ABOUT TWO FAIRIES GOD-PARENTS DRAGONS?!?"
... they wouldn't be above that.
Hope I helped!
Here's the link where I got the infos from.