You are going to need professional advice on how to proceed.
Yes, you should be paying yourself a salary. But you need to be aware that, as an owner of an S-corp, there are different rules that apply to your health insurance than there would be for your employees. Generally, the owner's health insurance premiums need to be included in the Box 1 of his W-2, and he can then deduct the premiums using the self-employed health insurance deduction on his 1040. Other employees will not have the premiums included on the W-2, and won't need to do anything special on their 1040.
But again, there are more details here that are needed, and you need to seek professional help.