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Unfortunately you’re never going to find an eCommerce package which has every feature and plugin required for your online shopfront. That’s why most eCommerce packages has the ability to use plugins for developers to add on custom functionality which doesn’t come out of the box. I’m not familiar with the functionality of the free one already suggested, but if it doesn’t suit your needs you will need to do (or pay for) some custom development.

I built a Xero plugin for a different eCommerce platform. It works on a timer, so once a day it will upload all the sales which intern creates new customers and invoices, including any transaction fees. Once the money is in your account it will auto match the invoices. The cost of development will be small compared to the time wasted manually creating invoices.