There is no such thing as a "SEP 401(k)." It's either a SEP IRA (which is a type of traditional IRA that you would contribute to from net profit from self-employment, a SIMPLE 401(k) (which is not an IRA) or a regular 401(k) (which is also not an IRA). An individual 401(k) that you contribute to from net profit from self-employment is a type of regular 401(k).
If your contributions are reported in box 12 of your W-2, enter the box 12 amounts only in box 12 of TurboTax's W-2 form, nowhere else in TurboTax.
