What I really need from you in order to give you a specific answer, is what the precise need is for your organization. For example, do you need to secure all mail between your different police departments and fire stations, or do you need to secure mail to and from specific people? Chances are it is some of both. Rather than give you a detailed step-by-step, which would be an extremely long answer, I want you to check out the Exchange...
Server 2003 message security guide.
There are a few Exchange 2003 exclusive references that will not apply to you like S/MIME for OWA and RPC over HTTP. But it is a terrific reference that should have everything you are looking for in it.
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