Recording bank fees and charges while receiving payments through PayPal is simple.
When your customer receives your invoice and chooses to pay for it through PayPal, the status of the invoice will change to Paid as soon as the payment has been received.
The payment received would be deposited into a bank account chosen by you while setting up the PayPal integration.
Assuming the invoice amount to be $100 and the Bank Fees and Charges to be $3, only the NET amount of $97 will appear in the bank feeds. This transaction will have to be matched with the corresponding invoice.
Ideally, the amount that you receive in your PayPal account is the net amount excluding bank fees. You can track the bank charges in the Bank Fees and Charges account by running the Account Transaction report in Zoho Books.