I know this is an old post, but someone might still be looking for answers.
1 & 3. On the User Documents tab in the QMC, select a document and then in the right hand pane select the Document Information tab and enter a Category. These categories will be shown in Access Point and you can group you files by these categories.
2. Since NTFS is the only authorization available in the SBE, we have used file permissions on the individual files to control who see what in Access Point. We will create groups with the appropriate users in them and then assign the appropriate group to the QVW file.