You must have the Scholarship Management User Role to apply scholarships to existing invoices.
After you have initially set up the Scholarship, added the redeemable products and the Families, you are able to apply scholarship funds to existing invoices for those individuals that qualify.
Here are the steps to add scholarship funds to existing invoices:
Open the invoice that you would like to apply scholarship funds to and click the "Apply Scholarship" button on the right.
After you click the Apply Scholarship button you will see the page to apply the funds. You will see the Scholarship name and the funds that are available for that family. Enter the amount you would like to apply to the open invoice and click Save.
After you click Save you will be directed back to the invoice and you will see the funds have been applied to the open invoice.