The best would be an additional opportunity of uploading files to the resource manager with their own ftp settings (like "Allowed Resource Types" for a resource manager category), so that they not use the same path as normal attachments.
For example IP.Board has such a function:
Since this does not seems to be possible, a method like the one I'll describe in the following would be at least a possibility:
When adding a resource, there is the button to upload a resource. It would be good to change this button or add an other one with a different functionality to upload the file on an other server, which is configured in the admin panel.
This file could be added as a link to a field like "External download URL", but this field should be invisible for the user. The user shouldn't know the direct link to the file. Hiding the direct links is really important, so that they need to use the resource manager to download files.
So for the resource manager the file should be handled like an external download URL and so it's independent of the attachments.
For a better idea and a good implementation I would definitly pay something.