taxomate will send multiple invoices to wave when a settlement spans multiple months or if the invoice has too many line items. Sometimes these invoices will contain a negative invoice. Unlike Xero or QuickBooks, Wave does not allow us to create a Bill via their API, which makes reconciling negative amounts more difficult in Wave.
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​STEP 1. Select Sales > Invoice and then choose the All Invoices tab.
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​STEP 2. If the negative invoice is marked as Unsent, select invoice and mark the invoice as sent.
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​STEP 3. For each of the invoices select Record Payment.
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​STEP 4. Select the Payment method and Payment account where you receive your Amazon payments and click Submit.
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​STEP 5. Remove Bank Payment from Wave
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Since you have already recorded payment for the invoice, you are going to need to remove the payment displayed in Wave from your connected bank account. If you don't do this, you will have duplicative payments in Wave and your books will be thrown off.
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You can delete your payment by going to Accounting > Transactions and select the particular payment and Delete.

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