Yea, includes will go a long way to clean up your code.
This is main event sheet for my current project:
It can still be a hassle at times, but if you use folders, includes and name things properly and consistently, it will go a long way to help you stay organized when you are nearing the end of your project.
Another technique I use is to create a debug event sheet as well. It basically serves as a test area that you delete before you complete your game. Once you have good code that you are happy with you add it into one of your include files and delete it out of the debug event sheet.