I've ended up creating an unscheduled journal entry, as I'm concerned that otherwise there will be a single payment amount hitting the bank account. Each Employee gets a payment in their name coming out of our bank account, rather than a total. So in order to reconcile, I created an Unscheduled Journal and added each employee with their payment amount debiting the bank account, and then the balancing item goes to "Payment" account where the payment is automatically taken from when running and finalising Pay Run.
This then balances the journal and reduces the "Payment" account to zero.
Just sharing my use of the functionality.