Yes, you can charge a processing or convenience fee to your clients. BQE CORE has the capability to include those fees in the invoice payment total when your client clicks the Pay Now button. BQE ePayments does not deduct processing fees per transaction but debits the total fees once monthly from a designated account. You can charge this fee on to your clients by enabling the ‘Pass processing fee to client’ option in Settings > ePayments. Check ePayments for details.
CORE allows you to specify the fee to be charged as a flat amount or a percentage. Check CORE Help Center for details.