LENR basically takes a second exposure of same length with the shutter closed to pick up any small inaccuracies in the sensor under dark conditions. These are then "subtracted" from the original exposure.
If you use, for example, a 30 sec exposure time then the camera takes a second "black" 30 sec exposure after the shutter closes to capture the background inaccuracies. your camera will appear to be non-responsive during this time. so be aware that when shooting a series of shots or using time lapse, the period of time between successive exposures needs to be more than twice the actual exposure time.
I have LENR enabled only in the long exposure/tripod menu bank of my settings. It is pointless to use it in normal shooting. As far as I know it is only activated when the shutter speed exceeds a certain time threshold - the manual will detail any restrictions.
Normal noise reduction carried out in-camera is different. It can be replaced with aftermarket software or enhanced and adjusted by using the "high quality" NR options in Nikon's Capture NX2 software (my preferred option because it gives a lot of options and fits seamlessly into my normal NX2 workflow.