So I assume you entered the bill for the freight. You need to set up the employee as a vendor. You will have to use some different form of their name so that is not a duplicate list entry.
Enter a vendor bill toggling the credit field at the top of the enter bill field and enter the amount that the employee paid. Go to pay bills. Select the vendor and apply the credit that shows at the bottom of that window. If not paid in full, swipe through the amount paid on the vendor screen and type in the amount that the employee paid.
Enter a bill for the amount that the employee paid with the employee as the vendor.