Changing from NTLM (Windows ACL permissions) to DMS the system moves from all doors open to all doors closed. Therefore, no one will have access to any documents/applications initially. You grant User access explicitly when using DMS mode. The shared files (meta/shared files) also stored alongside the QVW, will be used to control access to QlikView applications/documents when operating in DMS mode.
DMS will work with windows and non-windows users from an authorisation perspective (you can still hook into AD/LDAP directories services to view users). You need to enable DMS in QlikView Server via the Management Console. Once you select DMS, you grant user access per application, via the authorization tab displayed in the User Documents area of QlikView Management console.