Payment against Supplier Invoice for GL costs of goods sold

In my business I purchase goods for resale from suppliers and sell to customers.  Besides the cost of inventory, I allocate costs to the cost of goods sold account.  On the purchase order, the supplier is Joe's Supplier.  Below is an example of the GL items added:

Code    Item           # of items        Cost per Item       Total Cost:
5000     Cases        40                    $50                      $2,000      (using an inventory item)

(added GL items on the Purchases / Supplier invoice page):

Freight    $500
Customs Broker   $250
Fed Import Tax     $96
Local Freight        $100

When I allocate a $2000 payment on the Supplier invoice, it decreases the Payable amount but leaves a balance of the total of the GL amounts.  These services and taxes should not be payable to the supplier of the inventory.
How do I account for paying these amounts? 
Do I use the Payment link on the Banking and general ledger page?
If I do use the Payment link, do I debit the payment to accounts payable, or directly to the cost of goods sold account?