1.The one who answer the three economic questions in free market system is the Free Enterprises. - What to produce - For whom we produce it - How to produce it. All of these questions would be analyzed by the free enterprise based on the demand and supply in the market, so they could come up with appropriate product that they could turn into profit.
2. The difference is that in a command economy, the Government is the one that answers all three questions. In a command economy, the Government obtain total control on all the resources in the country, so private citizens basically do not have any say in all economic matters.