I LOVE the Godaddy Bookkeeping app for eBay and Amazon and Paypal sales. I also want to continue to use Shopify. Currently Godaddy Bookkeeping does not support ANY POS type software other than Paypal. If you're interested in this PLEASE contact them and let them know YOU WANT SHOPIFY INTEGRATION!!!
In the meantime you can use this free app:
To download your transactions in a bank transaction format (we combine a couple different shopify reports to make it) and then any accounting app (including Godaddy Bookkeeping) can easily import it.