Posting multiple invoices for one quantity

For service procurement, User is creating PO with one quantity and trying to post multiple invoices as the payments is to be made in installments.The system allows booking initial installments while doing MIRO by entering partial quantity and value. This fails at the time of booking last installment as there is some small variation due to partial receipts done earlier.

Adding tolerance limit wont solve the problem as the variance amount is not fixed.

Kindly suggest a way to handle this.