Are you already receiving money through Paypal? Great, you still will!
Are you also using Quickbooks Online with Paypal? That won't change either.
No matter what accounting software you currently use, payment data (in date ranges) can be exported anytime to a CSV file, making it simple to import revenue to any other software. Whether or not that is even necessary is really up to your accountant. A website with a built-in e-commerce solution makes third-party accounting software largely redundant for revenue received.