Create a new directory on your local machine. Extract all the files from the distributionkit (it's available in Windows Zip format and Unix tar.gz format) into this new directory (don't overwrite your existing directories, if you do so, you loose all your modifications and configuration files!

Use your favourite ftp or scp program to copy the files from your local computer to the webserver directory. When you copy the files to a subdirectory in your webserver's document directory, you are able to create a new copy of the site in a different subdirectory of your website without interfering with your current installation. When you are sure that there will always be only one (version of this) website on this webserver, you can copy the files to the root of your webserver's document directory.