As of firmware 3.0, you can now set multiple folders for push notification and syncing. It seem to work, because once the mail app gets focus, it already has the appropriate numbers for mail items in these directories. Something confusing though is the red-badges are still ONLY applied to INBOX items, (which is weird, almost like a bug or an oversight)...
Either way, my question is this ... can elert KNOW about the other sync'ed folders? If elert does something like poll the email db this should be possible, if it does something like look for the red-badges for notification then it will NOT be possible...
Just an idea/feature request.