At the end of the month (assuming you're a small employer) you calculate the employer contribution owing on this. Normally it matches the employee deductions for the month - although this can vary. The purpose of this article is to account for these deductions rather than explain in full how to run a Kiwisaver account.
Now this could be entered as a bill or it could be recorded as a journal. A bill is probably slightly easier - but your system might not let you record bill payments easily when you're also paying non-bills. So we'll explain using a journal but readers can, if their system allows, enter bills. Either way this should be entered with the date set to the last day of the same month as the deductions from wages. You debit an expense account for Kiwisaver contributions, and credit the liability account for Kiwisaver.
There are alternative ways you can do this. For example you could just debit wages - but if you're trying to reconcile wages between your payroll and general ledger systems, this would complicate things. Similarly you could credit a separate liability account for your contributions - but we don't feel there's usually significant benefit for the effort.
The balance of the Kiwisaver account at month end should be the amount you have to return to Kiwisaver in the return the following month. It has the employee deductions and your contribution in it. So when you make your payment to IRD, it will include the amount for PAYE and the amounts for Kiwisaver. The return separates these between employee contributions and employer contributions.
The latter is divided on the return into the net contribution ultimately paid to the member's scheme, and the ECST taken by IRD. So you could separate those into sub-accounts if you wanted to aid these calculations - but it's not necessary to get the accounting correct. If you did then you'd need to include separate lines splitting these in the payment to IRD. Then each sub-account should come to nil after the payment is made to IRD and entered.
If you follow these procedures then your accountant should not have major issues at year-end.