How does Turbo Tax handle a common pay agent agreement? We have employees that are due a refund on social security tax under this agreement, but turbo tax does not allow

Please clarify your question.  The only deduction allowed would be the amount of social security tax required to be withheld on the wages you paid. The refund would not be part of the tax return, rather a reimbursement for excess withholding to the employees. This would be an accounting issue, but not an tax issue.

I have a similar question.  I received two W2s because I was transferred between two companies of the same giant corporation.  This apparently caused a reset on my social security withholding and led to an overpayment.  Both W2s have the same EIN because both employers use a Common Pay Agent.

TurboTax does not appear to be able to treat the W2s as having come from two different employers because both W2s have the EIN of the Common Pay Agent.  It sounds like if TurboTax distinguished between the two employers, it would automatically put the overpayment on Schedule 3.

@inneedofsleep 

The Online software cannot handle this situation.

The Desktop software can...but you still have to enter the exact overpayment amount (just the excess $$ over $9114) manually, on the Schedule 3 worksheet, line 11, using the Desktop software's Forms Mode. 

(IF the two W-2 forms had different employer ID numbers, the $$ would have showed up there automatically.)

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Thank you!

I'm using the Desktop version and that worked perfectly!