You've only just begun learning the fundamentals of PHP, and already I'm throwing something else at you. Sorry (bows head in shame), that's just how it is; there are lots of moving pieces to your typical web application. We must take some to review databases. This is how we "remember" information. Or, in other words, if a user creates a handful of todo items, how will we remember those todos for when they return to our site next week? Well, the answer is through a database.
As for MySQL GUIs, you might consider any of the following:
The PHP Practitioner