As of the moment, @stevenjhdm, there isn't an integrated way of paying your liabilities and NEST payment. You're on the right track in paying them by writing a check for record-keeping. The actual payment must be maid directly from the HMRC
Meanwhile, @Louise_Green, we don't have the specific turn around time as to when the issue regarding with the payroll journals will be resolved. Rest assured that you'll be informed via email message once it is fixed.
Lastly, here's a few articles you can read for ideas about how the new payroll system works: QuickBooks Online Advanced Payroll Hub.
If you have any other concerns, know that you can always leave them in the comments. I'll be here to lend a hand.