IBM has release a list of paper's detailing the migration steps for migrating from WP V5.1 to WP V6.1
The first paper describes the steps and best practices for migrating an existing standalone WebSphere Portal 126.96.36.199 environment to a standalone WebSphere Portal V6.1 and should be followed by the majority of customers, even those in a Web Content Management environment.
The purpose of the second document is to provide a step by step guide for migrating IBM Workplace Web Content Management (WCM) version 188.8.131.52 to WebSphere Portal v6.1 – Content Build for Lotus® Web Content Management (also WCM). The foundation for this document is the initial release of the V6.1 Information Center with additional information based on the outcome and experiences of our pre-release testing. With this document, we provide more comprehensive guide and highlight some of the common pitfalls and mistakes when migrating.