Setting up multiple smaller websites: Horizontal or vertical?

Not sure if theis is the place to ask the question or not, but here goes:
I have to set up, say 6 websites for diferent departments. I want them all to use the same authentication object I built.
The authentication objects lives in the main directory. lets call it MainAuth.
I want the user to be able to authenticate once, then go to any of the 6 sites s/he is authorized to 'see'.
Question: Is there an advantage or disadvantage to build them inside the MainAuth website as /SiteA, /SiteB... I like the way I can generate menues that only show the choices a user is authorized to see.
-or-
Should I build each one outside the mainAuth directory, and (somehow) link them together?
 
Thanks
 
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