Those are a lot of questions, and many of them are not really suitable for a Q&A style format, and more of an in-depth tutorial or course.
In short, the guides you’ve read online are probably correct. You’ll just need to plug in the connection details (MySQL hostname, username, password, database name) and you can run your queries.
Please do note that our databases can only be accessed from code running on our servers, so you can’t test your PHP code (or Node.js) on your own computer with our database servers.
I think that this article may answer at least some of your questions:
Your website files should be uploaded to the htdocs
folder of your account. You can upload them with the file manager or with an FTP client of your choice (like FileZilla).