We have limited funding to support THERM (it is funded by the US Department of Energy) and so there is a bit of a learning curve to use it effectively because it is not as user friendly as it might be. And the DXF import is one of the oldest functionalities in the software -- we have never been able to prioritize making it more user friendly because there are always other features that take priority, mostly in terms of the actual thermal simulation functionality.
In terms of overlapping polygons from an Autocad import, you should delete the overlapping polygons, and then either draw them by hand or use the Fill tool if appropriate. The program will snap to the underlay points, so it's not as painful as it might sound.
What are you trying to model for your class?
Robin