Is there any way to manipualte properties outside of the Zope management area?
Yes, you can do it using the manage_addProperty method from dtml (or from Python/External Methods). In the same vein you can change them programmatically.
I have a lot of properties I need to add to a certain document and it's really time consuming to enter then one by one.
Also, Is there any way to arrange the order of properties?
For instance, I've added a bunch called story 1a through story1z, and story1r is misspelled as "stry1r". Currently, it seems to keep them in order I have to delete all the properties after the 1r property and enter them all again.
Keep them in order in what way? In the propertysheet? Then that's the only way. If you make your own form to edit the properties you might either call them directly, one by one, or gather them in a list, sort it, and then display them. Hope this makes sense Rik