It is recommended that you uninstall earlier versions of EndNote before upgrading. Make sure to first back up your library, styles, import filters or connection files. Follow the instructions to create a compressed library for this purpose, then see the upgrade instructions.
If you are currently working on a Word document using your EndNote library, you should unformat the document before upgrading to the newer version of EndNote. To do this in most versions of Word click "Remove Field Codes" from the EndNote toolbar. In Word 2007 with Endnote X5 or later, go to the EndNote tab and choose the "Convert Citations and Bibliography > Convert to Plain Text" command.
If you need more information on uninstalling and installing, check the EndNote FAQs.