They apply equally to all of the invoice's taxable tasks for sales tax rate 1 or 2. A standard, or default, sales tax rate can be entered into Preferences. This rate is copied to the billing information for any newly-added client. But it does not affect existing clients or invoices. It's simply a shortcut for setting up new clients more accurately.
Sales tax is charged on the total estimate, based on which job tasks are marked as taxable.
When an estimate is printed, it calculates sales tax with the rate from the Client file for each task that is marked as taxable. The task settings come directly from the job ticket. Task settings were copied from the Task Table to the job ticket when the job was added. Task settings can be edited on an individual job ticket, if necessary. Unlike an invoice, an estimate does not copy the sales tax rate to it.