The question I have is this... Everything in myscript.php is easy and works by itself... It creates a few variables does some number crunching and spits output. The problem I have is that I am not sure how to include the sapphire codebase in myscript.php such that I can get access to its classes / functions..
You could run sapphire like that. Eg your PHP not in the mysite folder but the autoloader will be a bit screwed so you would have to include the sapphire files in order in your code - similar to sapphire/main.php.
Why do you need external PHP files rather then building a sapphire project - with the code in the mysite/code folder?