STS is built on Eclipse so the debugger works the same way. You can see this tutorial for an overview
http://www.vogella.com/articles/EclipseDebugging/article.html
The main difference is you may not be running a
java application but rather a web app. To start TC-server click the 'Start the server in debug mode' button. It looks like a bug and is right next to the green play button in the servers tab in the lower left corner of the screen.