The scale function works by division.

If the model created is to be same size as the li_elite, but is about 6 times bigger in ms3d, the scale down factor would be 6.

Another option is to import the pilot model and try various scale ups of the
pilot using ms3d scale function until the proportions look correct.
If the pilot had to be scaled up by a factor of 12 to look ok in the ship model, the scale down of the ship would be 12 in the cmp exporter.

ColinS