On the emails not deleting properly, check the device. Go to messages, then options, then email reconciliation. Make sure that the settings are selected for both mailbox and handheld. Usually after a BES activation they are set to handheld only. Also that "mailbox wins" is set on conflicts.
As for the email folders, I was under the impression that the folders started syncing from the point of activation by default. In other words I'll bet if they take an email that the recieve now and move it into a folder and then go to the folder on the blackberry and hit reconcile now, it will show up in there. But anything from before activation wouldn't unless told to do so. Could be wrong on this.