There's really only two files you might need to require.
For regular Mardown:
require_once '/path/to/code/Michelf/Markdown.php';
$my_html = \Michelf\Markdown::defaultTransform($my_text);
Or for Markdown Extra:
require_once '/path/to/code/Michelf/MarkdownExtra.php';
$my_html = \Michelf\MarkdownExtra::defaultTransform($my_text);