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It depends on the configuration in your Exchange environment. More specifically, are you doing an inter- or intra-organizational migration? In an intra-organizational migration, you add Exchange servers into your existing sites and move mailboxes from server A to server B.
In an inter-organizational migration, you set up a brand new parallel infrastructure, which is a Greenfield approach to migrating users. It's a brand new, maybe even native forest, for which you have to create mailbox-enabled user objects and then migrate the content. (From an Active Directory perspective, you may also want or need to migrate the user objects from NT across with sidHistory.) In this scenario, you should leave original mailbox data in Exchange Server 5.5 and create copies of that data in the new Exchange organization. This can be accomplished using Microsoft's ExMerge tool or third-party tools that specialize in inter-organizational migrations.
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Related information from SearchExchange.com:
Expert Advice: Best approaches for upgrading Exchange 5.5 to 2003
Tip: Understanding Exchange 2003 mailbox migration methods
Tip: Preparing for an Exchange mailbox migration
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