As I understand your situation, your wife filed a Schedule C on your individual (Form 1040) tax return to report the income from her LLC. Your wife is only able to report her LLC income on Schedule C if the LLC is a single member LLC treated as a disregarded entity by the IRS.
If in fact the LLC is a multi-member LLC (e.g., you and your wife) the LLC must file a federal partnership tax return (Form 1065) and send each member a K-1. Those K-1s (instead of Schedule C) is how the LLC income would be reported on your individual tax return. If this is your circumstance, you'll need TurboTax Business to complete the Form 1065 for the LLC.
Your California Form 568 would be completed accordingly (i.e., either one member or two member).
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