That does sound odd and like you are trying to over complicate matters. I don't really see why you would need two databases just to hold two groups of users.
vB already comes with a very extensive user group system. Could you not just allow members to select between two different secondary groups to join when they register? That way it would split them into one of the groups or the other and you could assign the permissions within these two secondary groups that would affect what each group could see and do on the site.
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