After further analysis of the Fast Eye tool I've been able to show the .few files reference the ami settings files, in addition to providing the dll input parameters.
My problem now is that it appears that changing these parameters does not affect the simulation results. Any assistnace with this would be greatly appreciated.
I would recommend that you use the HyperLynx version 8.2 update 1 AMI channel analyzer. Since you have an AMI model and want to change the settings, using the AMI channel analyzer is the best choice. The newer HyperLynx version 8.2 update 1 has all of the latest features and fixes.