QuickBooks Online comes with platforms to both invoice your customers and receive payments from your customers. The advantage of using these platforms is that they are integrated into your accounting software. This helps achieve more accurate accrual based accounting and activates accounts receivable reports so you can see how much you are owed.
You can use one, both, or neither of these platforms. If you prefer to use a third party platform you will categorize the incoming money when you see it on the banking screen. You will have two databases. QuickBooks Online will be your database for income and expense activity that you use to view the performance of you company over time and the tax team uses to provide guidance and file returns. Your third party platform will be your database for customer information and invoice detail.