If you want to use the noise reduction without it hurting your audio, use Amplify on the section you want to sample the noise levels, set to -3dB (yep, you can use negative numbers). I always use a passage with *only* noise, for sampling.
After that, you apply Noise reduction at it gentlest setting.
This 'softens' up the effect in such a way, that it still does a pretty decent job, but with no ill effects on your audio quality.
But really, if you want best results there, don't mess with such plugins, and get Reaper or something similar, and do the job using EQ.