if you want to use the files created by Data Assist in the one main index page, you would need to use the Framework Builder extension to include them as plugins.
I still don't understand what you mean by:
"and I used the save as to make my website a Php but in the source file online the doc type is still Html."
the doc type wont change. using the. Using the .php extension only tells the webserver that the file may contain PHP code and should be processed by the PHP engine before sent to the client browser to execute the server side code.
the source code you see in the browser will still be HTML code. Some of that HTML code may be generated dynamically at run time by the php processor, such as retrieving info from a database and displaying it on the page.