As long as your "old" Sametime server is going to stay up for the duration of the migration, and there is no pressing need from an infrastructure point of view to do a gradual transition, you will probably find it easier to move everyone at once.
The main reason a user has a "Home" Sametime server specified in their person document is to maintain their individual "Connect Lists" (which are stored in vpuserinfo.nsf), and to allow them to log in to Sametime.
A user who does not have a Sametime server in their person document will be able to log into any server. However, a user who has an "*" (asterisk) in their SameTime server field will be prevented from logging in to any Sametime server in your domain.
If you are replicating the content of vpuserinfo.nsf between your servers, you will be maintaining the clients' connect lists on both servers.
When you are ready to do the move, change the "Instant Messaging Server" field in the Desktop policy document, which will modify the users Locations the next time they authenticate through Notes (normally on start-up) and run an agent on the required users to modify the SametimeServer field in the person document.
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