I think you’re misunderstanding how to use the Knowledge Base. I understand the updated UI is new and unfamiliar, and that this change can be frustrating.
You only add files once. Once you’ve added a file, on a Pickaxe by Pickaxe basis you can decide whether you want to connect that File (already uploaded) to the Pickaxe or not.
We will be making some tutorials this week. The new system should make upload easier (no double uploading) and increase the speed of retrieving Knowledge from the uploaded files.