My advice to you is not to make the mistake so many do of trying to turn PHP into something it isn't.
PHP is a Web-focused templating language allowing you to embed code inside HTML pages. It has a request lifecycle rather than being persistent (like Java servlets are). It's APIs are largely procedural in nature.
None of that is a problem.
Yet you'll find people who insist in trying to force object models, ORMs and other structures they're used to from C# or Java programming onto PHP and often it's a mistake.
To specifically answer your question, i tend to put all my queries (functions) in one file (or more if there are a lot of them, in which case I'll separate them out by database or by some functional separation) and the SQL is simply in heredocs in the functions. Not embedding SQL logic all over yoru code is useful.
You could put that SQL in text files and use file_get_contents()
on it but what do you gain?
There's just no point in hand-wringing and trying to apply principles from other languages and frameworks to PHP. Use PHP for what it's good at (or use something else). You'll be happier either way.