YES. You must keep the mysql database. The tables in there control everything relating to your users and databases.
It is bad practice to use your root user for web access. "root" should be limited to access only from localhost and should be kept for admin tasks, not a hard and fast rule, but that's what I do.
"root" is the superuser setup when you install. This user has access and permission to do anything and everything.
When creating a new project it is a good idea to create a separate database, and any users you might need for that project. Most of the time you will find that a user with SELECT, INSERT, UPDATE and DELETE privileges is plenty for getting started.
It is worth buying one of the many books on developing with PHP and mySQL. It really helps when you do not come from a programming background. Though these forums (and the devshed forums) provide a lot of help when getting started.
The php manual downloaded as a .chm is a great help too.
Good luck 😉