application of standard invoices to prepayment through API

The business scenario is that employee loans are handled through AP  prepayment invoices and recovery of the same is done through applying the standard invoice against the prepayment.

Since there is huge number of  recovery of employee months every month, entering manual standard invoice for each employee and applying the same against the prepayment invoice has become very tedious. In this back ground, we would like  to know  is it possible to bring in standard invoices through API and also apply the same against the prepayment invoice through API so that manual entry of standard invoices and application of the same against the prepayment invoice is avoided.