You can follow the steps below to let the IRS know that your were covered by health insurance all year that was not purchased from Health Care Marketplace. That is all they really want to know.
When you walk through the section for Healthcare under Health Insurance, the first question will be "Did you have health insurance coverage in 2016?". You should select "I had health insurance coverage all year".
The next screen will ask "Were you enrolled in a special plan from HealthCare.gov or another Marketplace in 2016?", you should select "No" there.
That will complete the part of the Health Insurance section you need to complete.