Hi Manos,
Thread moved to appropriate section
Joomla 1.5 introduced a new feature, the FTP Layer. The FTP Layer allows file operations (such as installing Extensions or updating the main configuration file) without having to make all the folders & files writable.. Not having to make your folders writable also adds to site & server security. This has been an issue on Linux & other Unix based platforms in respect of file permissions..
But TBH, I've seen FTP Layer, which being applicable to Linux Server users only & NOT for Windows ones, causing a lot of problems for many people.. You should rather opt for running suPHP on your VPS which negates the need for using the FTP layer & adds far more security to your Joomla site. With suPHP ownership issues as well as file write permissions are all things of the past.
suPHP for PHP Scripts is exactly what SuExec does for Perl files, that is, it makes them run under your specific user account, as opposed to the Apache user account. It consists of an Apache module (mod_suphp) & a setuid root binary (suphp) that is called by the Apache module to change the uid of the process executing the PHP interpreter. This allows us to better monitor the resource usage of accounts, as well as track down runaway script files with greater ease.. Also, it gives you the benefit of all your php scripts running 'in' your account. For some PHP applications this is a great help because now when you create files/folders from inside the script, they will be owned properly by your account & not the generic Apache user account.
The installation documentation of some php scripts will state that you should set the owner of the scripts as "nobody:nobody" or "apache:apache." Because of our use of suPHP, this is not the case. All files contained within your account (including php scripts) should be left as owned by your account..