When you enter the first 1099-MISC you will get a series of questions about the business (name, EIN, business code, etc.) From then on, you will have a "business" tab at the top of the screen as well as a "personal" tab. The business tab is where you will enter all the business income and expenses (depreciation, assets, etc.). The "business" tab is your schedule C. If you had two different businesses that you wanted on separate schedule Cs they would both go under the "business" tab.
The personal tab is where you will enter any other personal income (W-2, W-2G, 1099-R, 1099-B, 1099-INT, etc.) and your personal deductions (charity, mortgage, etc.)
