Paul,
Here are the answers to your questions:
1) The moveallreplicas.ps1 script is going to add the replica to the destination server, move the data and then remove the replica from the source server in one step. As long as you are ready to to this then you can run the script, even if you have already added some replicas to the destination server.
2) The moveallreplicas.ps1 is going to move the replica and data to the second server and so the step of syncing the folder is not needed. The source replica will not be removed until all data has been replicated over. You may have to dismount and remount the database on the source server once the hierarchy on the destination server knows about the replica list change. Clients that are still connected to the source public folder store are not automatically redirected so you want to force them to connect to the destination server so that they don't publish more source data delaying the sync. Please see: http://msexchangeteam.com/archive/2004/05/04/126015.aspx
Regards,
Charlotte