I've a remote office, connected via VPN LANtoLAN to the main office where is located a server with 2003 SBS. In the remote office there is a dozen of clients not joined to the domain, that use local DNS and gateway. There are also 2 clients joined to the domain. the only difference between them is the dns server, the local one for the standalone clients, the IP of the remote server for the domain clients. Everything works for both joined and stand alone clients, except for one little issue. The domain clients, even if it's specified in the lan configuration to use the local gateway, keep to use the "remote internet", wasting the VPN bandwidth that mainly has to bee used only for DNS queries and exchange.
The VPN (Zeroshell) connects two separate subnets, every connection between them is made by routing rules on the two firewalls.