For development, put the PHP files for your project right in your project folder. You can then use any text editor that you have installed on your system to edit them.
Next, add the file names to the manifest in Project Properties. When you do a Full Deploy, they will be copied to the server with the rest of your project.
The result is that your PHP files will be placed on the server, in the same folder as your app. Your app can call a PHP script by just giving the file name – no path name will be needed.