Yes, you will file two separate Schedule C's, one for you and one your spouse, even if you are in business together.
Enter the income and expense belonging to each person for their % of ownership of the business. If you don't have an official partnership agreement stating % of business owned by each of you, you can split business income and expenses 50/50 (or whatever is agreed upon by you both).
Here's helpful info for you:
https://blog.turbotax.intuit.com/income-and-investments/business-income/what-is-a-qualified-joint-ve...
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