The following example illustrates recording of your BAS payment to the ATO, or, alternately, receipt of a refund from the ATO.
In the example shown in Account Maintenance: Sample Journals - BAS Returns our sample Fund owed the ATO $915.96. This would have been rounded, on your BAS return, to $916.
To enter the payment (and the rounding), create the following Journal:

Note that the 4c rounding amount has been allocated to 5-1190 Overs and Unders.