My wife is working for the daycare at a church, and they take out federal taxes, but not SS. I am trying to figure out how to file that...any help would be appreciated

Cash payments provided to most all child/day care workers are considered wages and subject to employment taxes, so there's no getting around setting up payroll and doing things properly if you are a day care owner with paid helpers. Aslongas she receives a W2, then the ER must withhold her FICA and fed taxes; Child Care Workers are Almost Always EES. Independent contractors are few . Even very short-time or part-time workers are considered employees.

The general rule is that your wife is an independent contractor if she has the right to control or direct only the result of the work and not what will be done and how it will be done..If her ER treats her as a contractor, then they need to get her 1099 and she needs to pay self employment tax to the IRS; the ER doesn’t even need to withhold fed tax from her. In the case of self-employed workers and independent contractors, they pay the full 15.3% tax as self-employment taxes on Schedule SE that is filed with their tax return. Almost all employed and self-employed workers are covered by Social Security and are expected to pay FICA tax or self-employment taxes

Note; Generally, her ER must withhold income taxes, withhold and pay Social Security and Medicare taxes, and pay unemployment tax on wages paid to an EE. Her ER does not generally have to withhold or pay any taxes on payments to independent contractor aslong as your wife is a contractor.please visit the IRS website here for more info in detail; . Independent Contractor (Self-Employed) or Employee?

They consider her a employee, and they take out federal taxes, but since it is a religious organization, I guess they are exempt from SS, so they dont take that out...I am assuming we have to pay it, just not sure how to file it

A few churches don't withhold fica/mc.

It appears your wife needs to report the income on a sch C/Sch C-EZ and then use sch SE(aslongas the amount reported on Sch SE line 2 / 3 is $400 or exceeds $400)..

i guess your wife actually doesn't need to file Sch C however, she needs to file Sch SE for her SECA tax to the IRS as she is not subject to FICA tax as an EE.