USAePay is a payment gateway. Your ACH provider uses the USAePay to send (initiate debits) and receive transaction updates. Your ACH provider handles the sending of all debit and credit transactions, MCA Suite only pushes customer and billing schedule information to the ACH provider via the USAePay payment gateway. What time the actual transaction is submitted will vary by your provider.
MCA Suite has a nightly batch that goes to your ACH provider via the USAePay gateway to retrieve the status of transactions at 9:00pm Eastern.