Reg AR Refund Process through Auto Invoice

Hi,

Could someone explain as to how the Refund applications on the credit memo's trigger automatically when we run the Auto Invoice program? We are following the below process as of now and when we Import the credit memo transactions through Auto Invoice they Load successfully, however when we go and check for Applications--> The Refund Status isn't there and have to manually process refunds.

Step1: Only Credit Memo import through a Custom program to load data into Staging. (100% refunds - No Invoices in AR- These are being imported from SAP)

Step2: Run a Custom data validation program.

Step3: Run Autoinvoice Master program.