For templates that use chopping, one registers the positive spectra. Since there are many hot pixels, it is very helpful if there are several spectra to register and if these spectra are offset from one another.
The final step is optional and depends on how crowded the field is. One can use the two negative spectra that are either side of the positive spectrum to increase the S/N ratio of the observations. The end result will be a central positive spectrum with an exposure scaling of 4*DIT seconds, two negative spectra with an exposure scaling of 3*DIT seconds and two additional positive spectra with an exposure scaling of DIT seconds. This step should not be applied to images for which the non-linearity correction was done on the chopped frames, unless the negative beams have been treated correctly.