ummmm my gmail is connected to my berry and whenever i open new messages on my berry their marked as read on my email. i havnt tried it the other way around so i dont know about that but it should mark itself as read.....
Gmail IMAP via BIS will only sync one way (read/delete on BB will mark as read/deleted on server, but not the other way around). If you want two-way syncing, you'll have to wait until they upgrade BIS, or use the gmail app.