The tool divides the seed into four sections. Though they're numbered in a non-linear order in the program, the actual order of how they're displayed (i.e. the 3rd part is listed first) is the same order as how it'd be listed in PKHeX; I know this because I RNG'd a shiny before I touched the egg-seed field at all, where the first 8 numbers of the egg seed are the 3rd part etc.