To make this happen,someone with "Administer Filedepot" rights (in /admin/people/permissions), needs to set up top level files for user A and user B (by clicking on the New Folder button). Then click on A's folder in the right-hand pane and click "Permissions". That brings up a dialog that you can use to assign permissions to specific users. (Select user A and check the box for Folder Admin then delete any other access records.) Repeat for User B.
From then on, each User will be able to upload and download files in their own folders and see no one else's.
You will also want to give authenticated users "Access Filedepot" rights in /admin/people/permissions or set up a role with those rights and assign A and B to that role.