Note: This only applies to users on the Bonsai Tax add-on.
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The benefit of recording your past tax payments on Bonsai is that your estimated tax payments for the rest of the year will be far more accurate.

Bonsai takes the tax payments you've made for the year and adjusts the amounts you owe annually as well as quarterly.  So, by keeping your Bonsai accounting up-to-date you will have the most accurate picture of what taxes you may still owe for the year, if any.