Are simple ira deductions pre tax? Can this be changed in qb and will this effect my taxes ex. Quarterly and year end?

It's great to have you here in the Community, @beavertownmunici.

Yes, simple IRA is a pre-tax. Let's make sure that set up is correct so that the calculation will be correct. Let me give the step by step instructions on how to check the setup.

1. Go to the Lists menu, select the Payroll Item List. 
2. In the Payroll Item List page, click Payroll Item located in the lower part.
3. Choose New, then select Custom Setup and tap Next.
4. Select Deduction hit Next.
5. Enter the name of deduction, click Next.
6. Complete the information in the Agency for Employee-paid liability page, then hit Next.
7. In the Tax tracking type window, select the tax tracking-type classification that matches your plan type and click Next.
8. Put a check-mark next to any item(s) in the Payroll Item column that will be calculated after this deduction is taken.
9. Select Neither, tap Next.
10. Enter the needed information in the Default rate limit and click Finish. 

Check this article for the detailed guide on how to access custom set-up and it's related topics: Set up a payroll item for retirement benefits (401(K), Simple IRA, etc.)

After verifying the setup, you can now correct the year to date deductions in your account. There must be enough wages on the paycheck to cover the correction. You're unable to correct an amount that is more than the employee earned. 

In QuickBooks Desktop Payroll, you can correct year-to-date (YTD) additions or deductions on a paycheck when:

• payroll item with the wrong tax tracking type was used.
• payroll item used has the correct tax tracking type but the customer changed the checkmarks in the tax items screen, causing tax and wage base calculation error.

First, you'll need to create a payroll summary report for the current calendar year to determine the amount of money deducted using the old payroll item.

Second, edit the Tax Tracking Type into not in use, because you're unable to remove it from the list. Here's how:

1. Go to Lists, select the Payroll Item List.
2. Double click the item name in the pop-up window for Payroll List.
3. Put a checkmark in the Payroll item is inactive, then click Next three times.
4. Hit Finish. 

Third, in the employee profile, set up the new payroll item with the correct (addition/deduction) amount for future payrolls. Remove the old payroll item. 

Fourth, create a paycheck for the affected employee as part of the next payroll in the current year. If the employee is not due another paycheck, and if the item is a tax, deduction or company contribution, make a liability adjustment instead. After creating a paycheck, go to the Preview paycheck and enter the amount tax for YTD.

Here's how:

1. In the Paycheck, window click Open paycheck Detail.
2. Under Other Payroll Items, choose the old payroll item from the drop-down list. 
3. Enter the amount from the YTD Payroll Summary Report as a positive or negative number.

Check this article for the next steps. Proceed to number 7 in this link: Correct year-to-date (YTD) additions or deductions on a paycheck when the wrong tracking type was us...

Let me know if you have other questions. I'm here to help. Have a great day!