You need to get a fundamental idea in your head first.
You build an application, and it uses MySQL as a data source.
Users then use your application to do stuff. They don't connect your database as such. The connect to your application.
So you need a couple of things.
A database to hold your data
An application for users (and administrators) to connect to, to read (and write) to your database.
For database design check Peter Brawley's excellent website at
http://www.artfulsoftware.com/dbdesignbasics.html
For an application to drive your database, if you are going to use php, try googling "php secure login system".
It's NOT a trivial thing to build a secure system. Many have tried, and failed.
Good luck,
Barry.