It depends. When you are preparing the Federal Return, enter the amounts under the Federal Filing Copy as your main w-2. Code C has no significant meaning on the tax return, but codes D and W do. Code D is your 401K contribution, and code W is your HSA. These amounts must be reported in full for TurboTax to make any necessary calculations on the Federal Taxes portion of the program.
However, since you are filing a part-year Indiana return, the amounts on the city/local copy are the amounts allocated to your Indiana income. While I personally am unaware of any specific Indiana credits or deductions for these figures, you have them available if TurboTax asks in the Indiana return on the amounts of 401K or HSA employer contributions attributable to Indiana.
But, in order for your Federal return to be correctly calculated, enter the Federal Filing Copy amounts on your W-2 into the W-2 screen for TurboTax.
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