FlexDeploy download zip contains plugin jar files (application/plugins for Tomcat download and plugins for Weblogic download). You just need to copy plugins from download zip to plugins folder folder shown below & they will be automatically uploaded and activated on the Server startup.

This is very useful during initial install as well as when upgrading FlexDeploy, as there may be many new plugins or versions available as part of new FlexDeploy release, but you can use the procedure any time.