Hi Davide,
Thank you for reaching out to us! I believe there are two ways to simulate your waveguide in Interconnect: You can import the values mannually as you are describing or you can use the Exptort for Interconnect option on FDE:
You can follow this Waveguide (FDE) example for the second case. I believe that you should be accuate as long as you have the correct valu for the disperssion. We have several articles on how to calculate and export the disperssion: Algorithm to calculate dispersion and effective index in mode solution, Dispersion analysis of SOI waveguide,Sweep analysis for dispersion calculations. I am not quite sure what you mean about the cover index, regarding the cladding index however, I believe that since you are designing a waveguide on FDE (or elsewhere) the effective refractive index is what you are looking for. You can also reffer here in case you are looking to simulate an optical fiber: Optical Fiber (FIBER) - INTERCONNECT Element.
Finally you can't import an Mode source but you can import a Mode waveguide into interconnect: MODE Waveguide (WGD) - INTERCONNECT Element,Create MODE Waveguide Element.
I hope that was helpful.
Kind Regards,
Niki