Hello there, @12345CP.

I agree with your possible solution since QuickBooks will only determine the non-taxable and the taxable items if they were entered as separate line items by ticking and unticking the tax column when creating an invoice. 

Moreover, I'm adding this article as your reference in recording invoice payments in QBO: Record invoice payments in QuickBooks Online.

Return to this post if you have other concerns about your taxable and non-taxable items in QuickBooks Online. The Community is always here to help.