If your custom domain is of the form
app.example.com, you can register the custom domain in your Bubble app, in Settings -> Domain.
Bubble will instruct you to create a record at your registrar. The record will be of the form
Type: CNAME Name: myapp Value: app.bubble.io
You can enter this at your registrar:
Once Bubble and Cloudflare verify your domain has been updated, your custom domain will work!