Newbie lost in attempt to save file

I'm very new to FCKeditor and thought that I was getting on well with making it work until it came to saving an edited file.

I am using FCKeditor on an Apache server with PHP. I wrote some HTML which selected a file and loaded it into the editor. I could then edit it and decided to save the script using PHP fLoad()/fWrite only to find that the saved file appeared as raw HTML.

I then discovered that perhaps FCKeditor can save the script through FileManager but I'm unable to find any sample code to help me. I think that I've changed the congig files as explained elsewhere ... but how do I enable the save function. Any help much appreciated.