QB Issue Resolution:

set up a sales tax item for each rate
set up a sales tax rate for zero %

on the invoice or sales receipt

list all items that have the 5% rate, then a sub total item, and then the 5% sales tax item

list all items that have the 5.5% rate, then a sub total item, and then the 5.5 % sales tax item

in the customer tax code block at the bottom select the 0% sales tax rate

sales tax collection and reporting will be correct

Resolution for Issue 'Two sales taxes for same state agency' available: Yes (Solved).
Source: Intuit Community forum.

Two sales taxes for same state agency: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Tax
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Error Recovery for Tax [Canada]
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