If you have any stores connected to your Shopify (Amazon, ebay, etc.) do not sync with this app. If you have Trustfile syncing with Amazon directly it can determine the the taxes that are remitted directly by Amazon. If those orders come through the Shopify integration Trustfile will treat the orders as shopify orders and record them as tax that is due to the state. This not only doubles your taxes from the duplicate orders recorded, it also does not allow for taxes already remitted via amazon to be accounted for. I have spent weeks on this issue and finally received the only work around by avalara, recommending not using this app to synchronize the transactions.
Here is the final response from Avalara on my ticket:
I researched the issue and unfortunately, you were given misinformation. There's no way to exclude transactions from syncing into TrustFile, because it's a pure sync - all data goes in. AvaTax allows for that but not TrustFile.
The workaround would involve importing your Shopify transactions, less the Amazon transactions, into AvaTax instead of syncing.
Let me know if you have additional questions.
This app and the support are beyond terrible. I signed up for the free trial and ran the report for Q1. It only pulled in data for March. I called customer support and after being on hold for a long time they said they are not sure what happened and they would call me back. It has been 3 weeks and I have left multiple emails and messages and nobody responds. They have taken terrible service to a new level.