Hello @rwhalen1 ,
Yes, you would want to make your estimated tax payments based off of your net monthly income.
Keep in mind, these are estimated tax payments, so it is based off of your estimated net income. When you do file your tax return, you will fill out Schedule C. When filling out Schedule C, In part I,you will first report your Gross Income for the Year, Cost of Goods sold if applicable, to come to your gross income. Part II you will report your expenses for the year to determine your Net Income or Loss. Whether you used certain expenses to determine your Self employed taxes will not deter you from using those expenses when you actually file your tax return. Here are a couple of links that might help you.
The Self-Employment Tax
A Guide to Self-Employment Taxes for Contractors, Freelancers, and Beyond
Let me know if you have any additional questions, I'll be happy to help!
Cheers!
Holly W
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