Personally, I enjoy to do it manually.
PHP should not return both css and html code, or even better, it shoukd not return client-side code at all but rather dependencies to specific parts. You never want to modify a file that contains a lot of different things.
To separate css+html from the php code, what I usually do is a hierarchy done with include("..."); and include_once("..."). For example : include_once("header.php") > include("menu.php") > html semantic with css classes correctly initialized according to current context.
Then you import your css / js external scripts in header.php so that you never have to modify the whole thing unless everything changes or if you have a complete feature to add to the website. Same is possible for every sections of the website.
Hope this helps, for me it is incredibly reducing debug-time since everything important has to be done only once, then at the top of it, you can seperate as you wish.
ob_startorrequires..