TurboTax does prepare CO 104CR as part of the interview process.
In Colorado, you'll see an Other State Tax Credit Summary. New York should be there if you prepare your NY nonresident return first.
You are correct, You should "true up" your Colorado return. Not having tax withheld does not excuse you from a tax liability.
New York is aggressive about auditing out-of-state employees whose reporting office is in New York and who don't have a "bona fide" office elsewhere,.
TurboTax will submit all necessary forms with your Colorado e-file or include directions if you file by mail. To claim a credit on double taxed income you generally will need to provide your home state with a copy of your other state return showing income and tax reported to that state.
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