I am not sure why you could not simply enter the real estate as a business asset (nonresidential/commercial and depreciate it over 39 years) on your Schedule C and deduct all ordinary and necessary expenses related thereto.
If you then rented some portion, you could simply enter the rental income as such on Schedule E and allocate the expenses (in accordance with the lease (sublease) agreement).
Personally, and do not take this as anything other than my opinion, I would have set up the business as an S corporation and held title to the real estate in my own name or in the name of an LLC. This scenario gives you a couple of ways to reduce certain tax attributes: (a) pay yourself a salary and take a share of the net income as ordinary income (no FICA or SE tax) and (b) reduce the net income (and salary requirement) by taking a healthy rent deduction - [use your imagination here]
