Troubleshooting payroll check tax calculations

Verify exemption selections

Setup > Clients > Payroll Taxes tab:
In the Taxes section, are any of the checkboxes in the Wage Exempt column marked?
Setup > Payroll Items:
Are any items excluded from gross or net pay? Are any jurisdictions marked on the Tax Exemptions tab that should not be?
Setup > Employees > Payroll Taxes tab:
Is the Federal tax exempt checkbox marked? Is the Tax exempt checkbox under the State Withholding section marked? Are any of the checkboxes in the Wage Exempt column marked in the Taxes section?

FIT (Federal Income Tax)

Enter Transactions screen
The
Frequency
field is located within the
Handwritten/Check #
section.
Enter Batch Payroll Checks screen
The
Frequency
is located near the Payroll schedule field.
Setup > Clients > Payroll Information tab
Select the ellipsis near Payroll Schedules
The
Pay Frequency
is within the
Pay Schedule Information
section.

FICA-SS and FICA-MED

Run a Payroll Tax Summary - Detailed report.
OR, run a Payroll Journal with Taxable Wages.
Take the YTD taxable wage amount and calculate what the withholding should be.

In
Enter Transactions
, to to
Bank Account Mode
.
In the
Filter
, filter for a particular employee by ID or name.
Sort the list of transactions by date, and then locate the 1st payroll check for the year.
Select each payroll check and look for amounts in red for
FICA-SS
and
FICA-MED
.

Delete and re-enter the checks without making overrides.
Let Accounting CS make up for the past overrides, adjusting employer FICA-Med amounts as needed.
Continue to override the FICA amounts for the remainder of the year.

Close the Accounting CS application.
Right-click on the Accounting CS icon on your desktop and select
Properties
.
On the Compatibility tab, select the
Run this program as an administrator
checkbox.
Select
Apply
and
OK
.
Open Accounting CS and verify that the FICA taxes are calculating properly.

FUTA

Select Setup > Employees and select the Payroll Taxes tab.
Unmark the
Full FUTA rate
checkbox.

Multi-state calculations

Setup items in Accounting CS that may be affecting multi-state calculations

Select
Setup > Employees > Payroll Taxes
tab.
In the
State Withholding
section, select the
nonresident state
.
Select or unmark the
Nonresident exemption certificate
checkbox.

Select
Setup > Clients > Payroll Taxes
tab.
In the
State section
, select the state from the dropdown.
Select or unmark the
Client has nexus in this state
checkbox.
Alternatively, if a local tax is not calculating select the Local button and select or unmark the checkbox for the locality in the Nexus column.

Select
Setup > Clients > Main tab.
Verify that the correct address is marked as the
Taxing address
.
Select the
bars button
near the address to look up and validate the address.
If the client has more than 1 location, select the
Locations
button and make sure that the correct address is marked as the
Taxing address
for each location.
Select
Setup > Employees > Main tab
Make sure that the correct address is marked as the
Resident address
.
Select the
bars button
to the right of the first line of the address to look up and validate the address.

Select Setup > Employees > Main tab.
In the Locations and Departments section, make sure that the employee is assigned to the correct locations.

Select Setup > Payroll Items.
Find the pay item and edit it.
On the Tax Exemptions tab, look for anything that is marked.

Employees can be wage exempt in certain circumstances according to IRS Publication 15. The Wage Exempt checkbox should be marked ONLY if the employee meets the requirements for the circumstances described by the IRS. 
There are 2 places where the Wage Exempt checkbox can be marked: on the Payroll Taxes tab on Setup > Clients and Setup > Employees. Note that marking the Wage Exempt checkbox on Setup > Clients makes ALL employees' wage exempt.
Marking the Wage Exempt checkbox in the Taxes section indicates that the employee is not subject to that tax at all. Wages for that employee won’t be reported on payroll tax forms, or included on any reports generated from Accounting CS.

If you are unsure whether or not an employee qualifies to be tax exempt, refer to
IRS tax topic 753
.

Local withholdings

Use
Ohio's The Finder website
to determine what should be withheld according to the state.
Use
Pennsylvania's website
to determine what should be calculating according to the state.

Setup items in Accounting CS that may be affecting local tax calculations

Select Setup > Clients > Main tab and verify the existing client (work location) address by selecting the bars button to the right of the 1st line of the address.
Select Setup > Employees > Main tab and verify the existing employee (resident location) address by selecting the bars button to the right of the 1st line of the address.
Select Actions > Enter Transactions and start entering a payroll check for the employee. If you enter a check for $100.00, you can easily see the rates everything is calculating at.

Select Setup > Clients > Payroll Taxes tab.
In the State section, select the state from the dropdown menu.
Select Local and select or unmark the checkbox for the locality in the Nexus column.

Select Setup > Employees > Main tab.
In the Locations and Departments section, verify that the employee is assigned to the correct locations.

Select
Setup > Payroll Items
.
Find the pay item and edit it.
On the
Tax Exemptions
tab, look for anything that is marked.

Limits being ignored (FUTA or SUTA)

Multiple checks with the same payroll check date