If you want to edit your theme javascript, you first need to make sure you don't have any minified file published. By default, the theme.js.liquid  is minified because it gives better speed results. But each theme version also have the normal (un-minified) version of this file, called theme-debug.js.liquid . To edit the Javascript of your theme, simply copy the javascript (all the content) in the file  theme-debug.js.liquid and paste it in the file  theme.js.liquid.

Go to Theme > More Actions > Edit code and find the files called  theme-debug.js.liquid and  theme.js.liquid.