In version 5x, the database schema on which the repository was created should be backed up (DBA can help you in this), apart from any other additional document or universe domain created in 5x.
The repository in versions 5x/6x contains the three domains you have mentioned, which holds user security info along with universes,documents etc
If you login to supervisor and go to tools-repository, a list of one or more document and universe domains can be found with one security domain.
After the upgrade is done from 5x to 6x (by using a copy of 5x repository schema), the universe and document domain connection parameters should be changed in order to point to the new repository database… read on
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haider 
(BOB member since 2005-07-18)