After that you have downloaded the latest WPSpeed PRO release from your reserved area, you need simply to upload and install the package using the plugins installer. During the installation all files will be overwritten automatically and the plugin will be upgraded to the PRO version.

When you are prompt to install the plugin package, just click on the button 'Replace current with uploaded'.

After having updated the plugin, no settings or configuration will be lost. Only the files will be updated, but all settings will be preserved.