Does the question about contributing to a traditional IRA mean what you contributed on your paycheck (and therefore on your W2) or only additional contributions?

It would be referring to additional contributions that you made on your own to a Traditional IRA.

Typically, contributions made through your paycheck and reported on your W-2 would be to some sort of retirement plan (like a 401k) instead of a Traditional IRA.  

Enter amount shown in box 12 of your W-2 only in box 12 of TurboTax's W-2 form, nowhere else in TurboTax.