Proper settings for appserver's Role to user mapping?

With my LDAP external registry, I now have 2 places to map roles to users:
1) With LDAP groups
2) In the application server in the jazz WAR
Since the LDAP groups are examined in the admin screen, it seems clear that those need to be correct. But what should the proper settings be for the app server? Do they even need to be set any more? Is there a possibility that they could override the settings in LDAP?
1) With LDAP groups
2) In the application server in the jazz WAR
Since the LDAP groups are examined in the admin screen, it seems clear that those need to be correct. But what should the proper settings be for the app server? Do they even need to be set any more? Is there a possibility that they could override the settings in LDAP?