I don't believe direction of the holes really matters, or at least I haven't noticed. I prefer to but then vertical only because it makes it easier. Depending on the manufacturer of the frames, the grooves can be tight for the coroplast. In this case, I just squash the coroplast on the bench prior to installing and vertical holes make this easier (ie. push it in an offset manner and "fold" the divisions over)
As far as length, I would cut it as short as possible to get minimum extrusion since you plan on doing cut comb.