that itsn't quite correct.
The original idea was to deal with what happened to all those colonists left behind or caught by the cylons as they were pursuing the galactica.
The cylon original plan was to have all the human's exterminated. DeSantos was going to include John Colicos as Baltar who has been caught again by the cylons. They have had enough of him and are going to exterminate him. Facing death he choses what he sees as his only chance to survive at all, he comes up with the plan to have humans become part of the cylon machine race.
But since Colicos died, Desanto doesn't want anyone else to be Baltar out of respect. So this is assumed to be what the cylons do with humans now.
Apollo is lost to the fleet. He is seen at the very end of the pilot, as the camera zooms in you see his eye is mechanical with a red glow inside.
The plan was to have father vs son for a planned tv series. (His son, now called Orin, is commander of the Galactica) How would they get Apollo back? And how would Orin/Boxey deal with his father leading the cylons against humanity. Sort of like Darth/Luke or Locutus/Riker.
me and a few people were talking that this would be a great way to bring back Serina, the angel froom the ship of lights who helps guide Boxey to find his father and to give comfort to Apollo.