How To Properly Set Up Debugging?

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I'm using phpstorm.

Right now, the only debugging I know is coding, then reading my errors in the browser window... I'm guessing it's a trashy way to work.

 

I installed PHPstorm, I configured XDebug, I can run basic scripts and I'm able to read the output and debugging information in the IDE. However none of this works when I open an actual project. Project is utilizing MVC, so when I open a file that's buried somewhere inside one of the directories, my debugger is crying that it can't see certain classes and throws fatal errors. How do I configure my environment properly? I can't find what I need in PHPStorm help files