Thanks for joining the Community, @Matt Shirk.
I can help provide some information about using a third party program in tracking sales and payments that will sync into QuickBooks Online as well.
If your client is using a third party app that works with QuickBooks Online then yes, you can automatically import the transactions from that application into QBO by integration. To check if this is compatible, you can refer to this link: How do I find apps to connect to my QuickBooks Online?
If you can find the third-party app on the available list, you can contact them for help on how to integrate the two programs.
However, if the third party program is not on the list of compatible apps, then I'd suggest creating the sales tax entries manually into QuickBooks. Let me route you to this article for the two options on how to manually enter sales tax amount: https://quickbooks.intuit.com/community/Income-and-expenses/Enter-sales-tax-amount-manually/m-p/1857....
That should do it. As always you can contact our Online Care Support if you want someone to assist you in going through the steps.
You can also check out this link for more information about managing sales tax in QuickBooks: Sales tax in QuickBooks Online.
Please let me know if you have other questions about managing sales tax. I'm here to help.