Why would you invite several hassles by traveling with Nepalese passport when you have already taken US passport.
Like Jonny said, going to Nepal will not be an issue with Nepalese passport but coming to the US will be an issue. If you are thinking of showing Nepalese passport to enter Nepal and while returning, thinking of showing US passport, you cannot do that. It is because there will be no entry stamp or Nepalese visa in your US passport thus it will appear you entered Nepal illegally.
Just use US passport and your visit will be smooth.