When I use the pop-up flash to control my external flash wirelessly using Nikon's Advanced Wireless Lighting (AWL), I have been using the camera menus to control the flash ratios. I press menu, go to flash commander mode, then dial in the flash exposure compensation for the popup flash and the external flash. It works, but sometimes it's not fast enough to capture images of our toddler. I've sometimes thought how nice it would be not to have to go through the menus to adjust the flash intensity. Well, I just realized the function has been there all along. In fact there are two ways to do it.
1. If I'm in Program, Aperture Priority, or Shutter Priority, I can use the flash button on the body to adjust the FEC (hold down the flash button, then rotate the sub-dial). This function still works in wireless mode. When more than one flash is contributing to exposure (e.g., pop up and external), then the FEC adjustment is applied to all the flashes cumulatively. In practical terms, this lets you set up your ratios beforehand, then you just use the external FEC button to adjust overall flash exposure. For example, my SB-800 is my key light and is assigned to group A, in TTL mode with 0 FEC. My fill light is my pop-up, in TTL mode with -2.0 FEC. After I exit the menu, I take a shot. If it looks too bright, I adjust the external FEC button by -3 FEC let's say. The result will be the popup will have -5 FEC and the SB-800 in Group A will have -3 FEC. Note: I noticed that the metadata on the image will show up to -5 FEC but in the real world, the actual limit is -3 FEC.
2. If I'm in Manual exposure mode, I can use the same method above OR I can use the exposure compensation button. In the Nikon system, the exposure compensation affects both the ambient and the flash exposure. If you're in manual exposure and you change exposure compensation, it will just bias the meter and it won't change the ambient exposure, but it WILL affect the flash exposure compensation. As with the previous method, this change affects all flash groups and will adjust each group's FEC cumulatively.