May I suggest that you check the Lotus Notes Administrators Guids, section titled Installation ?
I'm sure you'll get plenty of good information there on how to proceed.
Otherwise, deploying is normally done in three steps :
1) copy the production server to a test server, upgrade the test server, create test client and test to ensure application functionality is still intact.
2) When functionality is confirmed by extensive testing, upgrade production server and go on alert mode to ensure minimal response time if issue does crop up.
3) When all aspects of application functionality have been confirmed to work correctly, upgrade the clients.
Always have a full backup before initiating an upgrade procedure.
Pascal.
I've got nothing to hide, and I'd very much like to keep that away from prying eyes.