If you qualify for the Business Use of the Home deduction, Form 8829 must be filed with you Form 1040 and Schedule C.
Without knowing more about your business activities, I cannot comment on your qualification for this deduction, but the existence of another office does raise cause for concern. Please read the following excerpt from a TurboTax FAQ, and also refer to: IRS Pub. 587 Business Use of Your Home
One requirement for the home office deduction is that you use a part of your home as your principal place of business.
This doesn't necessarily mean that the majority of your business activities need to take place in your home office.
What it means is that you use your home office regularly and exclusively to administer or manage your business and that substantial administration or management activities for your business are not conducted at any other fixed location.
Example: Larry just started a new consulting business, and has set aside a spare bedroom as his office which he only uses for business purposes. About 85% of his time is spent outside the home, meeting potential clients in various restaurants and coffee shops. However, he does all his scheduling, planning, and bookkeeping from his home office. These administrative and managerial activities qualify his home office as his principal place of business, even though he's spending the majority of his time outside of his home office.
If you have a regular job in addition to self-employment: The "principal place of business" question refers to your self-employment activities, not your regular job.