As you seem to be aware of, If you and your spouse are both partners, each of you must complete and file your own Schedule SE (Form 1040), Self-Employment Tax, to report your partnership net earnings (loss) from self-employment. You are both general partners (not necessarily the managing partner). If you indicate your wife is a limited partner, the software will not treat her share of income as self-employment income and will not generate a Schedule SE. In the business software you should indicate that your wife is a general partner so it will properly flow through to your personal return.
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