Newforma does have the ability to setup multiple folders that your users can file emails into on a project level. 

The Pro’s of this setup is that this can conform closer to the way the users are filing today and these additional folders will be created under the default folder for the Drag and drop filing method.

The Con’s for this setup include the ability for emails to be filed and duplicates created as Newforma cannot parse duplicates that are placed in different folders.