I use Kashflow and have an app that links in directly. Automatically creates customer, and sales invoice. Have had this extended to automatically create purchase orders to supplier as well.
The problem with the existing shopify reports is that you need to combine a couple reports to get what you need for accounting. That's why we created this and you can use it for free:
We built it to keep track of our own shopify purchases and fees and thought we might as well share it.