Although at first glance it might appear as if your eBay / Etsy fees are being duplicated, but when we look closer, they're usually not.not.
The eBay / Etsy fees are recorded as an expense when they are incurred (for example, when you list an item or sell an item). These are categorized as "eBay Fees" or "Etsy Fees" on the Expenses tab.
The payment made to eBay from PayPal or to Etsy from Paypal, on the other hand, is a transfer of funds from PayPal to eBay / Etsy, not an an actual expense. These transactions should be categorized as "Transfer Out" of PayPal and in to eBay / Etsy and therefore will not affect your overall business profit or loss.