Adding E2K server in a E5.5 network

I am a state agency and am thinking about installing E2K on a Win2K server. I want to connect to the State’s Exchange 5.5 network. They are not currently running any Win2K servers. I’m wondering if I setup AD, if this will affect the State’s future network configuration. Should I install E5.5 and wait on the State to move to Win2K and AD? Any thoughts or comments are greatly appreciated.