NOTE You must have installed WordPress 2.9.2 FIRST before installing and or updating to any higher version.
Updating to version 3.x from 2.9.2 is simple as downloading the zip file and SFTP the files right over top of the previous files in the wordpress folder. Make sure you backup the database and the whole /private/var/www/wordpress folder just in case, before updating.
Login (wp-admin) and WordPress may ask to update the database if it is necessary. Install the latest version of Quick Cache, plug-ins and you are good to go.