gap,
Bear with me as we go through this first part of working with the sorter as you have it now.
That is a version I did not want to release as I could fore see the very questions your asking.
It will fix your issues now once you understand the limitations and how to edit things.
Future versions will make all this a non-issue and will just be a 'click-done'
type thing.
If you've gotten this far? Open the obj file you just exported and search for use.
You should have 2. Those will be listed as material_0 and material_1
There should also be a new mtl file.
Now you can run the sorter on the obj file exported from Meshlab.