Under Deductions & Credits, TurboTax asks about contributing to a Traditional IRA. Is this referring to our company plan which deducts from our payroll?

No.

The company plan is almost certainly a "retirement plan", not an IRA. For example, it may be a 401(k) plan (very common).

Retirement plans are not IRAs. IRAs are "retirement accounts" that are owned by the individual. Retirement plans are managed by someone like your employer.

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

Thanks, this is what I was looking for!