A few thoughts come to mind. One, you can bring your cheese out early to warm up before using so that it will cook faster (it may help though to slice the cheese while it is cold, if you are using the cheese in sliced form). Second, put the cheese (sliced or otherwise) on top of the sauce so as to be more exposed to direct heat. Third, select a cheese that is known for its quick browning characteristics. Fourth, let the pizza bake longer if it isn't in danger of burning on the bottom. Fifth, you can turn on the broiler and move the pizza under the broiler for the final minute or two of baking, and pull out the pizza when the cheeses are suitably browned. The broiler can be turned on when the pizza goes into the oven, or part way through the bake time, which is what I do when I use the two-stone method. You may have to experiment with positioning of the stones and use of the broiler to get the best results from your particular oven.