You have the option to invoice retentions at the time of creating your customer's progress claim, or having the retention accrued. The accrued retentions can then be invoiced and processed as a group when the project is complete. The method you choose depends on what your customer wants you to do and/or whether you plan to remit any GST applicable for the retention component; if you invoice the retention amount then the subsequent GST charged is payable by you to the tax office, but your customer may not pay you that component when they pay the main invoice claim amount.
In this manual it is assumed that retentions are accrued and then processed in a batch at the job's completion. This is because, if the customer is going to pay the retention when the claim is created, why have any retention in the first place? However, MJC should cover all options for you.