Well, you would go into cPanel (or LPCP) and tell it to create a database under a certain name. Then you would create a "user" (with password) and grant them access to this database and grant them "privileges" they need to perform various operations. On the PHP side, make sure you use the MySQLi library, rather than the obsolete MySQL library. You can either google mysql example and mysql tutorial and see some tutorials, or you can obtain a free application (blog, store, forum, etc.) and browse the code to Learn By ExampleTM. The problem with this is that many commercial-grade applications (whether free or not) tend to use some pretty complicated code for highest performance, so they may not be good for a rank beginner. You probably should stick to tutorial pages. You will need to decide on a few simple tables to start off, create .sql code to IMPORT via phpMyAdmin (or use phpMyAdmin's DB editor directly), to create and start populating the database tables. Finally, you can write some PHP code to do an INSERT INTO and a SELECT query. You might want to start off with procedural calls, but you should work your way up to OO coding before long, as that's the preferred way in MySQLi. Before long, you should be starting to make sense of application code that you study.
Not knowing your coding proficiency, your understanding of RDBMS and SQL, or your level of interest and energy, that's about all I can suggest. I think most tutorials would do as good a job as I could in giving some sample code.