Hi,
I think you're referring to the chord names that the software transcribes for you from the MIDI file. There are a few different things you can do:
1. Try selecting different staves to include in the chord name analysis. Sometimes a particular instrument might add a lot of "busy" notes, but not really contribute to the foundational chord structure so much.
2. Try selecting a different "Style" when doing the chord analysis such as "Easy", which uses the most basic chord types.
3. After doing the chord name analysis, you can directly edit any of the chord names by double-clicking it and changing it to something simpler that sounds good to your ear (eg. C6 to C)
Enjoy!
Sherry