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By all means, keep it in the same Exchange organization if you can. That way you can use the full ExDeploy tools like MoveMailbox. Now you've already moved your NT4 accounts to Active Directory (AD), you should probably upgrade AD to 2003. Then follow the steps in ExDeploy.
When you insert the Exchange 2003 CD, it does not run setup directly, but takes you into the Exchange Deployment Tools. These are a cross between a wizard, multiple checklists and a resource library. Note that there is an update to this that came out a few months ago at the same time as SP1; download the AllTools selection under downloads from www.microsoft.com/exchange.
You can also run and look at ExDeploy at any time so you can use it to plan and understand your migration. For really great in-depth docs, check out the Exchange 2003 Technical Documentation Library at the same link.
More information from SearchExchange.com:
Learning Guide: Exchange migration
Article: Many Microsoft customers clinging to Exchange 5.5
Tip Library: Migration advice
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