Here's a quote which should help:
Ellone: "You can't change the past. I just found that out. When I was kidnapped, Uncle Laguna went on a journey to find me... But because he did, Uncle Laguna wasn't able to be by Raine's side when she died. Rained wanted to show Laguna her new born baby... Raine kept calling out for Laguna. So no matter what, I wanted Laguna to stay in the village... But it didn't work."

But, I think Ellone was sent back to Winhill before Raine died. Laguna says: "It was a mistake to send Ellone alone back to Raine. Raine died, and Elle was sent to the orphanage. If I had only gone to Winhill with Elle... I would've bee able to see Raine one last time. Raine was dead. Ellone, missing. My job kept me busy. I was left here thinking about this and that and before I knew it, all this time had passed. Well, that's about it."

Also, the scene where Laguna is at the orphanage is before he rescues Ellone from Esthar. Edea asks Laguna about "this Ellone", to which Laguna replies:
"She was kidnapped by Esthar soldiers. I've been travelling, tryin' all I can to get inside Esthar, but...".

Putting the last two quotes together, it would seem that Laguna only found out he had a son when he saw Ellone again. The timeline should go something like this then:

----Ellone's parents die
----Ellone adopted by Raine
----Laguna and the Lunatic Pandora problem
----Raine rescues Laguna
----Raine & Laguna make Squall (a bit of an euphenism there)
----Ellone kidnapped by Esthar soldiers (this could have
occured before the making of Squall)
----Laguna begins his search for Ellone
----Goes to the orphanage looking for her
----Enters Esthar, saves Ellone, removes Adel
----Sends Ellone home, becomes President
----Raine gives birth to Squall, dies shortly afterwards
----Ellone & Squall sent to the orphanage.