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Proper way to configure FarApp & Avalara Avatax for Amazon transactions?

What is the best/proper way to configure FarApp & Avalara Avatax for handling Amazon transactions?

Amazon is our marketplace facilitator for most states so they calculate, collect and remit sales taxes on our behalf, yet we still need Avalara to keep track of each transaction, including Amazon sales, so that it can keep tabs on our economic nexus thresholds for each state that will eventually need registration and filling of sales taxes in those states. Avalara had us create an advanced rule for marketplace remits exclusion so that Amazon transactions are excluded from our sales tax liabilities reports.

The problem is that in NetSuite, if we bring in the sales taxes charged on the Amazon transactions through FarApp, Avalara still calculates sales taxes and sometimes their amount is off/different than what Amazon calculates. This causes open invoices and AR with an incorrectly recorded open balance.

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