We would like to upload documents for everyone in the account as well as user-specific documents, can this be done?
Both Shared (Account Documents) and Private (User Documents) can easily be uploaded by the Admin within the Staff module. Managers are able to upload User Documents.
Also, when creating an Account Document there are three options for privacy, Admins Only, Admins & Managers or Admins, Managers & Employees. To set those privacies simply select "Create Folder" and then upload the document.