Hi Vince,
was a while ago now! Can't really remember!
Yes it is a single server setup.
All I can say is any time you are preparing to do a major version upgrade, (4.5.0 to 5.0.0 for example), make absolutely sure that you have a full working backup of both Email accounts and Zimbra files before starting.
Best to build on a new Server whilst also keeping the original live if you have the luxury of a second server to use. This way you already have a complete backup (the original server) in case it goes wrong on the new one without affecting Users.
I think the whole thing took me a few weeks to get just right but I took my time.
I believe I built the new server with the same version as the original on it (4.5.9) then used IMAPsync, Rsync, etc to make an exact copy on the new server and then I upgraded the new server to 5.0.9.
As I said, was a while ago and can't remember all the details but I think I followed a guide on the Forums or Wiki for this.
Good luck with it, doing it this way takes a while but is pretty safe. Please could others comment if I got this badly wrong
Looking forward to Zimbra version 6 for it's features but not looking forward to upgrading to it!
Russ