6
I can't say that there isn't a tutorial for that somewhere, but I'm not aware of one.
It looks like most of your questions can be answered here - but it's in bits and pieces. (you've probably seen these already):
How does the theme work in relation to the rest of the system?
https://xoops.org/modules/smartfaq/faq.php?faqid=244
What is the purpose of the templates_c directory?
https://xoops.org/modules/smartfaq/faq.php?faqid=182
How do I learn about developing my own theme? (has a couple of relevant facts.)
https://xoops.org/modules/smartfaq/faq.php?faqid=207
But usually, if you make a change to a module's .php files, you'll see it as soon as you refresh your page. Sometimes - very rarely, I find that I have to set my site to the default theme to see the changes. That has only happened twice that I recall.