Having the S corp does not prevent you from claiming the self-employed health insurance deduction with respect to one or both of the partnerships just as you have done in the past. Make sure that your partnerships show sufficient amounts with code A in box 14 to cover the deductible portion of self-employment taxes and the self-employed health insurance deduction. When entering the Schedules K-1 (Form 1065), make sure to mark the box on the Describe the Partnership page to indicate that you personally paid for health insurance.
