You should wait until your first return has been fully processed before you amend. So, if you are expecting a refund, wait until it has been received. If you have a balance due, give it a couple of weeks before amending so that your amended return will be filed before the April 15th deadline.
You will enter the second Schedule C in the same section as where the first one was added. There should be an option to add another Schedule C or another business when you revisit that section after starting the amended return. Just be sure to indicate that the second business belongs to your spouse when you begin the process of entering the information.
Here is a reference for how to amend your return:
How do I amend my federal tax return for this year?
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