any time you install a new version of an extension, the previous version should be uninstalled. yes, Dreamweaver will give you the option to install the extension over the already installed one, but this should always be avoided.
The Upgrading an extension video:
watch?feature=player_profilepage&v=ArZk7Lfrdkg
walks through the process.
Uninstalling the extension will not change any code on your created pages.