You can achieve this requirement through FI clearing rule(transaction code OBIA and OBIB).

For example, you want to populate same payment reference value from vendor invoice document to payment document.

Create FI Clearing Rule

Transaction Code: OBIA

Click on New Entries, enter Clearing Rule (two characters ) and Description.

Save.

Select clearing rule  and click on “Clearing Rule Fields” of Dialog structure on left hand side.

Click on New Entries, enter  Item number 1 and Field KIDNO for payment reference.

Save the entry.

Maintain Maintenance view for assigning FI clearing rules

Transaction Code: OBIB

Click on new entries and select account type (K for vendor D for customer and S for GL)& assign your clearing rule which you created through OBIA.

Now setting has been done for populating payment reference value from  invoice document to payment document for vendor.

Post incoming invoice

Transaction Code: FB60

During posting an invoice, click on payment tab and enter payment reference value.

Check Payment reference value in Vendor Line Item Report

Transaction Code: FBL1N

Post outgoing Payment

Transaction Code: F110 or F-53

Check value for payment reference for cleared and clearing item

Transaction Code: FBL1N