The night sky spectrum (background) is saved in the Sky-###.fits 2D spectrum file. Centroids are computed at the positions of known night sky emission lines. The list of possible lines are taken from the file SkyLineDataBase/sky.results[.ESI] (wavelengths are in Angstroms in air (76cm/15deg)).
A table of the centroid results and the pixel shift from the arclamp wavelength scale is shown in the log file. A mean shift is computed (rejecting outliers) and is applied to the object wavelength scale unless there is a problem with the computation, or the exposure is short (<420s), or there are too few lines (<5), or the ratio of RMS to measured shift is greater than 4. You can also prevent this shift from being applied by using the '-noskyshift' option in MAKEE. You can override the computed value using the 'skyshift=' option, where the value is in pixels.
For ESI, the wavelength scale is fairly stable and often the sky shift is not applied. If you bracket your exposure with arclamp exposures, you may not need a skyline shift. You should compare the RMS of the skylines to the difference in the wavelength solution of the arclamps.