This won't happen automatically; you will have to file two separate Schedule C's.
Each spouse reports his or her share of the business income and expenses (50/50, 75/25, etc). As you enter the business, you will be asked to Tell Us About your Business. You will do this process twice, once for each spouse.
On the information for the spouse that received the 1099's, you will enter the full amount of the 1099's, but that spouse will have an expense you will enter on the screen that says Enter Business Expenses Not Yet Reported. Here you will enter the description of - QJV Spouse portion of Income received on 1099. The amount will be whatever percentage you decide. So if it's 50/50, you will enter half the amount of the 1099's.
For the spouse that did not receive the 1099's, you will say No to any questions asking if you received a form. You will enter your half of the 1099 income under Income or Sales for your Schedule C.
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