Since you're rooted, you can get Xposed Framework to get most/all your customizations, including your toggles.
You should be able to stop individual apps from posting notifications in the app info settings. I think that came around in 4.1, hopefully Samsung/AT&T/Rogers didn't disable that for whatever reason. If I understand you correctly, though, you don't want any email notification in the shade but you still want something in the bar? Not sure how to go about that, but you can always get a launcher with an unread count that shows up on the email icon.