If you want to manage groups for LDAP users locally in FishEye/Crucible (as opposed to managing them on the LDAP server only), you should use the 'Read only, with local groups' LDAP server configuration. This will allow you to set up and manage local groups in FishEye/Crucible, while still synchronizing the users and groups from the LDAP server. See the documentation for more details.
Alternatively you might want to consider using delegated authentication. In this mode there is no explicit user synchronization. Instead you can either manually add users, or create them when they authenticate for the first time. You can either copy their groups from the LDAP server on authentication, or manage them entirely in FishEye/Crucible.
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