Sometimes settlements are sent to QuickBooks with fees and costs being higher than the revenue (negative settlements). This usually occurs when the settlements span more than one month, and split settlements are turned on in your settings or if you are a new seller.
If you owe Amazon money for the settlement period, the easiest way to reconcile would be to send a Journal Entry for that one settlement period:
If you would like to use credit memos instead, here are the steps to do so:
STEP 1. Create an expense by going to New and under Vendors and select Expense.
STEP 2. Select amazon.com customer (or applicable marketplace) as the Payee and your credit card account as the Payment Account (or account you make the payment from).
For the payment date, select the date of the charge.
For category select Accounts Receivable and then enter the amount of charge to your credit card under Amount.
STEP 3. Go to Receive Payment and select the Expense you created and Credit Memo so they balance each other out to 0. For credit card accounts you deposit to Undeposited Funds. Select Save and close.
This is how your screen will look if there is just a credit memo:
If you have both a credit memo and invoice your screen will look like this:
STEP 4. Head back over to your bank/credit card account and find the transaction where you paid Amazon.
If you paid with your bank account select Match.
If you paid with your credit card, you can Exclude the transaction.