It really depends on how your company is set up. However, as a sole owner you cannot pay yourself via a 1099. Any payments out to you that are not paying FICA taxes would be considered "distributions" and cannot be deducted from the companies Net Income. However, if you make a W2 payment to yourself, that can be deducted. You have to be sure to understand the difference and how it interacts with how your company is set up.
All-in-All, you cannot pay yourself as a 1099 contractor if you are the owner of the company.