How can I get by the Federal and State Tax line in the Payroll if my firm never took those out and made my Employee 1099?

Hello there, @kssnacksone.

Let me share some information on how you can track your 1099 income.

Since your Federal taxes were not deducted from your 1099 income, you'd want to record it in full in QuickBooks. Then, categorize it as Schedule C Business Income.

QuickBooks automatically calculates  your estimated self-employment taxes which includes your income, Social Security, and Medicare taxes. You can read through this article for more detailed insights: How QuickBooks Self-Employed tracks self-employment taxes.

On the other hand, state estimated taxes isn't currently not supported in QuickBooks Self-employed. However, you can add it as a business transaction in QuickBooks for recording purposes.  You can check these articles on how you can use QuickBooks to manage your taxes:

• QuickBooks Self-Employed annual tax guide
• Get quarterly and annual tax info from QuickBooks Self-Employed
• Schedule C and expense categories in QuickBooks Self-Employed

Lastly, I'd suggest consulting with an accountant so you'd guided accurately in tracking your self-employed income and expenses. 

Keep in touch if you have other questions or you need more assistance with using QuickBooks Self-Employed. I've got your back. Have a good day and keep safe.