I work for a non profit who do not pay into social security. They take extra Fed. Where do I pay into Social Security?

You do not pay into Social Security when the employer does not tax your wages for Social Security taxes.

Even if the employer classifies us as Self-Employed? I have entered all my information into TurboTax and in years past they had different questions for Schedule SE and this year it is very different. TT is saying I do not need to worry about Schedule SE even though my W-2 shows I had 0 SS and Medicare tax witheld.

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@NMURPHY wrote:

Even if the employer classifies us as Self-Employed? I have entered all my information into TurboTax and in years past they had different questions for Schedule SE and this year it is very different. TT is saying I do not need to worry about Schedule SE even though my W-2 shows I had 0 SS and Medicare tax witheld.

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Then you should be using the Self-Employed section of the program.  Net self-employment income pays SE taxes of 15.3% of the net.

See this TurboTax support FAQ for Schedule C - https://ttlc.intuit.com/turbotax-support/en-us/help-article/import-export-data-files/enter-schedule-c/L5Fz3j5us_US_en_US?uid=m70si9i4

On your W2 is box 13 checked for Statutory employee checked?  I think that makes you fill out schedule C for self employment.  Was it checked in the past but not this year?