Add the file to /assets/config.json
For example, here is what mine looks look
"entry": {
"main": [
"./scripts/main.js",
"./styles/main.scss"
],
"customizer": [
"./scripts/customizer.js"
],
"story-creator": [
"./scripts/story-creator.js"
]
},
Where 'story-creator.js is the custom js file to be added.
Then yarn run build
And then enqueue the file from src/setup.php
I believe this is covered pretty well in the docs https://github.com/roots/docs/blob/sage-9/sage/theme-development-and-building.md