It really depends on whether your wife materially participates in the business. If she does not participate in the business, then you really shouldn't be splitting your business into 2 schedule Cs just so that she can show income. However, if she does participate in the business, then you should be either splitting the business income, or paying her as a W-2 employee, or paying her as a 1099 subcontractor, so that she accumulates credits in the Social Security system.
Whether you can fix this retroactively would be a subject for a professional tax advisor. Going forward, Carl gave you 2 good suggestions on how to include her in the business. An additional suggestion would be that instead of paying her as a W-2 employee, you could pay her as a 1099 subcontractor. Then she would file a schedule C for her subcontracting income and expenses while you would file a schedule C for your main business, and include her subcontractor payments as one of your expenses.
