Right now all my tests live in a happy.js file. Now that I'm starting to write end to end tests for non happy path functionality I'm realizing I need to organize these tests better.
How would you recommend organizing the e2e files?
There is no universal approach for organizing test structure. It strongly depends on the complexity of your project. For example, you can see how tests are organized in the TestCafe repository
In addition, I recommend you refer to the Using Page Model article to see how to create an abstraction of a tested page and use it in test code to refer to page elements.