If you are currently moving all emails to your task manager creating your own to do lists, when you categorize your email you have already processed it so in seem useless to keep it stored in your email folders.
After the issue is done you can archive it in a folder. Keep in ming that as less folders you have better! So if you can work it out with one general archive that's the way to go!
It seems to me that you have experienced a gigantic step forward: you have managed to adapt GTD method to your own outlook usage, therefore creating a couple of "must have" folders that really are of no use to you! Keep working on your system and be alert to things that serve you (and reinforce them) and things that don't (and drop them).
Wish you the best! Be productive!