Any changes that you make in the Jet Cutting operation screen is what will be applied in the G code. Those changes will not affect your tool settings.
It can be helpful to make those changes in the Jet Cutting operation, if you are trying to tune your settings. You can make the change in the Operation, without changing your tool settings, and then go back and change the tool after you find what works.
If I understand correctly, when you select a tool for the operation it will load the saved parameters. You can then change them in the operation and that will override the tool settings.
Improve your cuts making changes to the operation and when you are happy, create / update the tool.