Has anyone tried using suitescript to apply a journal (acting like a payment) to an invoice or a bill?

You can apply Journal to invoice or bill without any customization..you just need to select the account and the customer in the entity column in journal. In the invoice, click Edit then in the apply tab in the credit section you'll see the Journal - select it and Save

Yes. We are aware of that. But we would like to do it via script if possible.