Laguna was away in Esthar when Raine died, so Squall ended up at the orphanage. I don't remember clearly, but I think Ellone ended up at the orphanage because Laguna didn't think he could care for her as a father whilst also getting involved in crazy stuff on another continent. The orphanage was one of the places he looked for Ellone after her abduction, which would explain why he chose to send Ellone there. He probably never knew that his son was there too.