Since Amazon collects and pays the sales tax for the Marketplace Facilitator Tax, you may want to set the Filing Frequency in QuickBooks Online to Yearly for those states. This is so that you'll only need to make one payment per year in QuickBooks Online for those states affected by the Marketplace Facilitator Tax.
You can pay sales tax liability in QuickBooks Online on the taxes collected and submitted by Amazon on your behalf using the Amazon Marketplace Tax account.
If you've already set the frequency for monthly, you can always Edit the Sales Tax Settings and change it to Yearly.
If you collect tax for your state, you should set the filing frequency to whatever your state requires. Talk to your accountant if you have any questions about taxes.