Yes, you should include improvements and home-office-specific expenditures when setting up your Home Office Deduction.
Your home and any improvements (that increase its fair market value) are entered separately as Home Office Assets. See screenshot #1 below of the Home Asset Summary page (click to enlarge).
The renovations specific to the home office are also entered as a separate asset (be sure to check the box to indicate this asset is limited to the home office - screenshot #2).
For more help, look for the blue links throughout the Home Office Deduction section.
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