Are you using the stock Samsung email client on the phone? If so, they're supposed to sync (if not, they won't), but you're right, my watch says I have more unread email than my phone or outlook (which match). I just deleted a bunch of emails though, so I don't know how long it will take the watch to figure it out. I've never really paid attention to this (how often they sync up or if they agree). I just checked again and the number on the watch is dropping but they still don't agree. My outlook and phone didn't agree either in one case (outlook said I had one email read that the phone showed as unread in an IMAP account).
Looks like a bug, because when I delete emails from the watch they delete on the phone, so there's definitely communication happening, but the unread count is wrong. I wonder if there's a pattern to it, like emails that get deleted from the phone when the watch is out of range (or standalone for us 3g users) that become orphaned on the watch.