I can answer this one!

(I just asked and it was answered and it works)
So, if you're running the latest version, anything moved from the junk folder to the inbox will be tagged as something to train the ham (not spam) account. Anything moved into the junk folder will be tagged as something to train the spam account.
You can verify that this is happening by choosing "View Mail" in the admin console for either one of the spam/ham accounts. (It's really pretty cool, if I mark something as junk with my Entourage or with my Treo SnaperMail, it gets moved to the junk folder and Zimbra learns.)
kazoo