There are 3 ways of doing that, this ways works with FTP or if you are hosting the files.
PhpSgeX have an autoupdater, so you must only replace older files with new ones!
WARNING: be sure to not delete config.php (make a backup!)
Download the new version.
Simply drag & drop the new versions files (in the phpsgex folder) to the directory in with you have installed PhpSgeX
DONE!
Download the new version.
Delete all files (of your current working copy of PhpSgeX) EXCEPT config.php and upload new files to the working copy directory!
DONE!
This way it's recomended for devs because code on the repository may have more bugs!
You must simply checkout the repository and then you can update it!