I work for a company where it is basically me and the owner. We have no company handbook or any type of company policies or rules or anything. I am expecting a baby in about 2 weeks and want to go back to work as soon as possible. My boss is worried about how long I will be out and looking for someone "temporary" for while I am gone. Is my job protected at all? If it is not available when I am ready to go back, will I qualify for unemployment?

Considering the size of your company, you do not have any job protection. Your employer can replace you. As far as unemployment is concerned, I believe that you would be eligible if you continue to work until your physically unable to do so. You may wish to verify that with the state.