Proper database design is the only way your application will be efficient, flexible, and easy to manage and maintain. An important aspect of database design is to use relationships between tables instead of throwing all your data into one long flat file. Types of relationships include one-to-one, one-to-many, and many-to-many.
Using relationships to properly organize your data is called normalization. There are many levels of normalization, but the primary levels are the first, second, and third normal forms. Each level has a rule or two that must be followed. Following all of the rules will help ensure that your database is well organized and flexible.
To take an idea from inception through to fruition, you should follow a design process. This process essentially says "think before you act." Discuss rules, requirements, and objectives, and then create the final version of your normalized tables.
In the next hour, you'll get underway with using MySQL through any number of interfaces.