Your best bet is to unify your networking around an IP/Ethernet standard. Support for IP networking over Ethernet has been available for the Mac for quite a while, and will allow the two sites to communicate much more easily. Once you have a network that is capable of interoperating, you have many choices for connectivity between the sites. If real-time, low-latency perfomance is paramount (i.e. you are running video or audio between the sites), you should consider a committed-bandwith solution, such as fractional T1, frame relay, or MPLS. If cost is the driving factor, consider an IP-based VPN and local ISPs. If you lack the technical expertise to set up and maintain such a network, there are many consultants and service providers that will be able to help you get started.
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