Make sure you have the built-in Speedlight set to TTL flash mode. When you are in Manual exposure mode, you will want to under expose the ambinent per the meter and the Speedlight will make up the difference.
In P, S, and A exposure modes the camera will under expose the ambient automatically and allow the Speedlight to make up the difference. When using flash, I would recommend using Manual ISO. Flash and Auto ISO don't play well together. Good Luck and Enjoy your Nikons!