Regarding the S corp owner, you are correct.  This is required by the IRS to be reported in box 1 of the W-2, but should NOT be included in Box 3 or 5.  We use it for medical, dental and vision as all are health insurance subject to a pre-tax condition.  It would not be the same as any other payroll calculation because health insurance for a regular employee is not reportable in box 1.  So, it would require a separate calculation NOT subject to Social Security, Medicare, FUTA.  Technically it is not subject to income taxes either because it is currently allowed as a deduction before taxable wages on the individual tax return, however we have ours set to withhold as it hits box 1.  In our state, it IS subject to SUTA, so I can not speak to the state treatment in your environment.  You should contact your company accountant/payroll provider on that treatment.  Finally, it is marked as a box 14 item on the W-2 with the code of 2%SEHI. 

So just to clarify... it will not let me setup a calculation that is calculation type "employer cost" and subject it to payroll taxes. The way I have all other employees setup is employer cost that is credited to health insurance payable, and when the premiums are paid, they reduce the liability account.

So for the owners, do i need to keep the original calculation for them for the premiums and then add a separate calculation to report the premiums as wages? 

The employees deduction is subject to all taxes unless it is a section 125 cafeteria plan. Then no taxes apply.   

We have a stand alone calculation for this issue and it is a calculation type of add/deduct taxable.  We also credit against the health insurance payable account.