The diagram seems to be lost in the post if your could edit the post and add that in please.
Also if you could add details on your current BGP architecture or if this is a greenfield for BGP?
How are you interfacing the routes from this setup to the rest of your network?
Are there BGP neighbors downstream of the site connections or is this a simple hub/spoke setup?
From your description I would assume you won't need to worry about the Q-in-Q at all but that part would be strictly on your provider network with you connecting via the designated customer S vlan at each site. But want to confirm you are not running Q-in-Q over carrier ethernet for some reason.
Steve Puluka BSEET - Juniper Ambassador IP Architect - DQE Communications Pittsburgh, PA (Metro Ethernet & ISP) http://puluka.com/home