I want to integrate Vault with Amplify Storage so I can use S3 as the backend. How can I override the upload (and other functions) to use my own?
You can use any needed custom logic to perform the uploading on your specific backend.
https://docs.dhtmlx.com/vault/uploading_files.html
I want to customize how the frontend is calling the backend, that document is about creating a backend.
Please try to use the beforeUpload event to control and break the default uploading process on your frontend:
https://docs.dhtmlx.com/vault/api__vault_beforeuploadfile_event.html