You are on the right track. When entering the information into TurboTax, treat it as three separate units. That will give you the most flexibility when it comes to reporting the income and expenses and making changes in the future.
You should not use any of the expenses from the unit 'in-progress' to offset income from the unit that is currently rented. That would not be keeping them separate from one another. You will need to wait until the 'in-progress' unit has been placed in service by being advertised and available for rent to deduct any expenses related to it. Your renovation costs will be added to the basis for depreciation for that unit.
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