Is there some guide out there that describes how the PHP internals?
Sounds to me like you're you should look for resources on PHP Internal development. Looking for this information elsewhere will be really scattered.
I suggest picking up a PHP Core development book from your local book store and giving it a read. PHP.net has an underdeveloped beginners reference if you wanted to start there.
This excellent although somewhat outdated book by Sara Golemon has answers to the most of your questions. Otherwise, the best way to learn php internals is to compile a debug version of it and run it step by step under a debugger. I did it once and it was an exciting experience.