Warehouse
Unlike other MMOs where a warehouse actually stores excess resources, your warehouse works differently. It saves resources for you to rebuild your city if you are beaten in an attack. The higher the level of your warehouse the more resources you will have saved after an attack has taken place which you can use to train troops for a counterattack. The level of your resource buildings determines the amount you can hold, not your warehouse.
Marketplace
Use the marketplace to buy and sell the resources that you need. The price for each varies day to day depending upon demand. Each resource will take approximately thirty minutes to reach you once ordered. If your marketplace is upgraded you can do more transactions at one time.
How To Increase Production Levels
Besides upgrading your resources through building leveling you can increase your production in two ways. First, your academy can research production bonuses that will raise your resource production 10% per level. Resource technologies should be researched first so you are really increasing your production significantly.