Thanks for the kind words, I'm glad it is proving useful for you.
I would start with a simple file. Just one or two lifting surfaces, similar resolution, fixed wake in both tools. Make the models as similar as possible. Do they agree or differ?
Make sure the coefficients are non-dimensionalized in the same way. Make sure the moment center (CG) is in the same place.
Then I would start adding in the differences in the models. Relaxed wake, more complex geometry, etc. This approach usually leads to understanding what the models do differently.
Rob