It depends on if you are using actual expenses or the simple calculation. If you choose to use actual expenses you should use the expenses from each of your homes for the time you lived there. If you choose to use the simple calculation, and you lived 6 months in each home, you can average the square footage of both your office space as well as your whole home to enter into TurboTax. For example, if your first office space was 150 square feet of your 2500 square foot home and your second office space was 200 square feet of your 3000 square foot home you would enter 175 (150+200 = 350/2 = 175) for your office square footage and 2750 (2500+3000 = 5500/2 = 2750) for the whole house square footage.
For the steps to enter your home office deduction see Where do I enter the home office deduction?
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