Either method should work for threading up a new halyard – but whatever you do make sure that the existing halyards are taut inside the mast. I have known a few instances where the existing wire halyards have been left slack and spiral round the inside of the mast. You then thread your new spinny halyard down the middle of this and all works well until you then pull the other sails up and all the halyards twist up together, leaving you wondering why you need to apply about 200lbs tension to pull the spinnaker up!
As regards the pulley block usage, I’d just go with whichever gives the best lead for all 3, but if you swap them over take the heel plug right off and have a good look up the mast (using a torch perhaps) to again ensure that none of the halyards are twisted up together on their way down.
Perhaps main halyard on one side, cleating onto a rack just above, then jib halyard in the middle onto a centrally mounted highfield lever, and spinny on the other side leading down the boat might work best?