The upgrade of any Domino server needs to be organized task. You should have a checklist for the upgrade and a predefined upgrade sequence.
At a high level, the recommended upgrade sequence is:
1. Domino Administration Client for all your administrators involved in the upgrading project
2. Domino Directory design
3. Domino Administration servers
4. Hubs servers
5. Spoke servers
a. Mail servers
b. Application servers
c. Web servers
6. Notes Clients
7. Mail template and application designs
By upgrading servers before clients, and clients before applications, you minimize disruption to users and business activities. With this approach, users will not see any Notes/Domino 6 features until their clients can utilize them; and conversely, users will not attempt to take advantage of Notes/Domino 6 features until their servers can handle them. However, your infrastructure, as well as your administrators, are able to take advantage of the Domino 6 features and functionality.