Making the decision on whether to generate invoices and collect payments through accounting software or through an eCommerce platform will generally depend on the business structure. Businesses completing orders through an eCommerce platform may find it easier to handle payments at that level. It can provide more transparency to your buyers to see invoices generated there, and be able to quickly make payments, rather than be in a completely separate accounting system. However, some businesses have orders coming in from a variety of sources, and in those scenarios, it can make it easier for the business to centralize payment collection in the accounting software.