Yes, you'd prepare two Schedule Cs, one for each business, but only one Schedule SE. If you had two or more businesses subject to self-employment tax, your net earnings from self-employment are the combined net earnings from all of your businesses. If you had a loss in one business, it reduces the income from another. If you are married, filing a joint return, and each spouse has self-employment income, then there would be 2 Schedule C's and 2 Schedule SEs.
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