You can still file jointly. If you have been using turbotax online, you will need to upgrade to the self-employed version once you start your tax return next year, but this is done within your ongoing account.
Being self-employed means, in most cases, add a schedule C to the tax return in the name of the spouse with the business income. Schedule C reports gross income and expenses, and calculates taxable profit, which flows to the main form 1040 where it is combined with your other income, personal deductions and credits, dependents, and so on.
However, if she has formed a partnership with someone who is not her spouse (either as an LLC or unincorporated partnership), then she must file a form 1065 partnership return. The 1065 will also generate a K-1 income statement for each partner that is included on the partner's personal tax return. Form 1065 can only be prepared with Turbotax for Business, which is a separate program only available for PC, there is no online or Mac version. The deadline for a 1065 is March 15, not April 15, and there is a substantial late fee.
Turbotax is not designed to track business income and expenses and calculate any estimated tax payments that might be required. For that, you may want to use a business accounting program such as Quickbooks.
