You don't really embed php into HTML... php is a server-side language - meaning it doesn't get interpreted by your browser the way css/javascript/html does. Instead it's executed on the web server - you'll never see php code.
The benefit of this is that you can do all kinds of logic and manipulation of data, and then send some formatted HTML to the browser for display the results.
.phtml and .php are the same thing though you really don't see .phtml too much anymore. On the server side, you can configure the extension to use for php.
That help?