You would have to prepare separate federal returns as married-separate and enter the itemized deductions on your federal return. You would have to allocate the deductions between spouses. You then only file the state returns, as the federal return you file will be the one you prepared as married-joint. So, you would have to prepare three federal returns but only submit one of them.
You may find it easier and less expensive to use the desktop TurboTax as you can prepare all the returns using the same product. You can use the Tax Tools option on your left menu bar while you are working on your return to then bring up Tools, which will have an option to Save your return to your computer so you don't need to start your online return over in the desktop version of TurboTax.
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