These days there are many companies providing merchant credit card services. Not all handle the fees in the same way. Below are some that we have experience with and how they treat the fees.
Paypal, Shopify, Stripe, Amazon and Square Up all deduct the fees from the deposits before they go into your bank account. This means you have to make an entry to add the merchant fees back to your sales and book to bank fees or create sales receipts and book the fee on the form. If you do not do this, then your sales are understated and your expenses are understated.
American Express Merchant, Bank of America Merchant and QuickBooks Payments aka Intuit Merchant Services all deposit the gross amount of the sale and the merchant fee separate. This is ideal and is less work.