I usually fly by the seat of my pants when building my databases. However, my new project is going to need quite a bit of planning. I never went to school for database development so I have no formal training on the planning process.
Is there any good software, methodologies for planning these things out?
Stick with the first few normal forms when designing your schema if you don't know what you're doing. Odds are it will allow you to make changes easier than any other method when you realize your design mistakes later on.
When in doubt, feel free to ask for opinions. The easiest method of visualizing a database design is to use Entity Relationship Diagrams (ER Diagrams) and it also allows us to easily see what your design looks like without sifting through code.
Download and build your database using MySQL's Workbench tool. Will help you build and maintain the database.