PHP was build specially for back-end development, and it's a good programming language. You can also use Python, which is also a very powerful and easy to learn programming language used for back-end. There is another good server-side programming language called Ruby, or if you have to work with a lot of texts you can use Perl, which was influenced by C/C++. If you want to create a database you should use SQL, so there are a lot of options, all that matters is which of the languages is easier for you and which does what you need to.
You can learn all of them from CodeCademy (https://www.codecademy.com/ ).
Hope this post helps you
Wahdat -- the XDK does not dictate what you use on your backend, there is no tightly-coupled connection between your mobile app and your server backend. You should use a RESTful API (standard HTTP network transactions) to communicate with your backend. So the backend can use whatever works best for the backend. The XDK creates standard Cordova (aka PhoneGap) apps, so solutions you find that work with a Cordova or PhoneGap app also apply to your XDK app.
p.s. You cannot develop your server side code with the XDK, it is only designed to develop IoT Node.js and Cordova HTML5 apps.
If you want to learn more about backend development here you can find a short tutorial about it https://www.codeproject.com/Articles/759094/Step-by-Step-PHP-Tutorials-for-Beginners-Creating
În order to create a PHP file you don't need a special development enviroment( such as Intel XDK) because the Php backend ia just file written in PHP, without the need of any compilation. You can use any text editor you want ( Notepad, Notepad++, Sublime Text, etc)
PHP is running in the server that hosts it.