It’s quite a common accounting scenario…
Effectively what you do is create a dummy bank account (under merchant section) called something like “Amazon Marketplace” and then you’d tag your sales invoices as paid into here, along with any Amazon fees.
Whenever you have remittance payments into your current account from Amazon, you tag these as transfers from the Amazon Marketplace merchant account.
Handling payments from merchant accounts
The above guide refers to payment providers but the concept is much the same.