Lulu here from the Shopify Support team. Thanks for reaching out here, and I'll be more than happy to help you out.
The most popular sales tax app I find is TaxJar. This app can prepare and file sales tax returns in minutes, it can automate sales tax reports by state and local tax jurisdiction and it can also handle your returns.
In regards to setting the tax rate, you can set up Shopify to automatically handle most common sales tax calculations. You can also set up tax overrides to address unique tax laws and situations. Shopify uses many default sales tax rates, which are updated regularly. If you use the default rates, then you need to confirm that they are current and correct for your particular circumstances by speaking to your accountant. You can override them whenever necessary.
We have a great guide on taxes in our help centre that you can read through here. I hope this helps but if you have any other questions, please don't hesitate to reach back out.
Also, with Black Friday and Cyber Monday coming up, we have put together this Black Friday Checklist. It is full of tips and tricks to make the most of the busiest online season so be sure to give it a read!
Lulu | Social Care @ Shopify
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Just keep in mind Taxjar cannot handle Colorado and our 700 different taxing jurisdictions. Taxjar will only file the state return, that leaves you to file the remaining 699 yourself. I have several eCommerce clients I file sales tax for in my home state of Colorado due to the special districts and home rulers this app can't handle.