I was just thinking. After rescuing Ellone from Adel and Esthar altogether, Laguna is forced to stay because everyone wants him for president (for some reason I'll never understand). In this, he sends Ellone back to Winhill, to be with Raine, but it's also never said how she gets there, and with who, because I hardly doubt Laguna would let Ellone travel alone while she was so young.
That led me to think Kiros might be the one who took her back, and as such, he still got to see Raine with Squall, who explained Laguna was the father and all that, and that's how he knows. Obviously, Kiros can't leave Laguna alone for long or that guy gets completely lost, so he had to go back, but he might have even told this too to Laguna (I think it's implied at some point that Laguna does know Squall is his son, I just can't remember exactly when, if it does happen. I haven't got that far yet in the game).
Another possibility I thought about was Ward taking Ellone, because we all know Laguna can't read Ward's expressions, so Ward was the one to know, and then he told them, probably wrote it down, or Kiros had to translate it to Laguna (if he does truly know, I really can't remember. If Laguna doesn't ever get to know Squall's his son, then it's a secret between Ward and Kiros).
As for Kiros's comment "You have your mother's eyes.", as long as he knows Raine is the mother, he can do this comment in both situations, because he's already been to Winhill before, during the third dream sequence, where Ward isn't present, thus he'd inevitably know Raine nonetheless and would be able to make the comparison.
It has to be eitheir Kiros or Ward to take Ellone, because Laguna wouldn't trust anyone else with Ellone but them, and I don't think both would go because both know leaving Laguna alone is a big NO.
But what do y'all say? Do you think this makes sense, and if so, is there's some more information to help us know which scenario is true?