Here's what I teach students as a baseline for flash at my workshops (you can get much more elaborate, but this addresses the main issues you face with fill flash on Nikon bodies):
- Camera set to Aperture-priority exposure mode. Gets rid of the aperture limitations in Program exposure mode.
- Camera set to Slow Sync or Rear Sync. Gets rid of the bottom end shutter speed limitation of 1/60 in aperture-priority exposure mode.
- Flash set to Standard TTL (press the Mode button on flash until only TTL shows in the mode indicator on the flash LCD, or use spot metering on the camera as it sets the same thing). Gets rid of camera-induced flash compensation level, which is unknown.
- Flash set to the fill level you want via flash exposure compensation, typically -1.0 stop for people, or Galen Rowell's "magic" -1.7 value for outdoor scenic fill. Allows you to control the fill level rather than the camera.
Generally, I can get to the balance I seek between ambient and flash very quickly using these steps.
Note that recent Nikon DSLRs (D4, D800, D600, D7100) have a Custom Setting option for completely separating ambient exposure compensation from flash exposure compensation (other Nikon DSLRs have impacts that interact with each other as you change one of the compensations). Generally, I recommend that you leave this option set to separate the compensations.