The exchange mailstore used in both VM and UM are the same. The main diff is that the licensing for VM is provided by cisco; another way of saying is that you get run-time license for exchange when you buy VM.
When you get UM, it is assumed that you already have existing exchange servers, and existing windows/exch accounts that you would like to use for the unity. Cisco does not provide exchange run-time licenses with UM.
So, to answer your question, I am assuming that you are going to join your brand new Unity server into an existing domain, with Exchange 2000 built on-box with Unity. If so, when you create a new vm account, you will be creating a vm-only windows/exchange account on the Unity server. There will be two windows/exchange account per Unity-subscriber.
