Matt, iTunes is the point of contact for all things iPhone. It syncs mail setup details so you don't have to manually configure anything on the iPhone if you so choose. It will also sync changes to your settings so that you can change stuff on the desktop and it will be reflected on the iPhone the next time you sync. iTunes knows about mail. It just doesn't do anything about the actual messages.

I didn't "want" to use iTunes. I was just under the impression iTunes handled messages and thought that's what it would be doing when I did a sync - which I already do for apps, contacts and calendars.

I as asking for input based on iPhone-sepcific experience on how I might set this up, not documenting how I was going to do it. I hadn't made up my mind yet, and the only reason I mentioned pop3 was to let everyone know how I currently had my desktop set up.

Everything is now set up, but I can't seem to get my 2700 sent items up to the server's sent mail folder nor can I seem to get my previous 2800 received messages up to the server's "older" folder.