Using 3D Sicer + SlicerIGT + Plus toolkit for building navigation system using Atracsys tracker should be fairly straightforward, once you got to know these components.
You can build a complete navigation system without writing a single line of code, which should be sufficient for phantom experiments. You can create a slicelet if you have the complete workflow sorted out and ready to do patient cases (or phantom experiments with time constraints).
Check out SlicerIGT tutorials and let us know if you have any specific questions.