So long as you got the databases combined and the values in the globals files combined you should be ok to use both of these in the same site. The admin pages rely on the same access rules from Security Assist, and the other shared files like the validations should be fine.
I did a quick test of this and what I found was naming my admin folders as admin_cms and admin_users worked ok. You could potentially combine the admin pages but you would need to account for the two admin index pages, for the users reg the admin index page shows user stats.
