This is pretty basic editing stuff... very easy.
The most obvious way would be to use your razor tool to cut the clip into different sections. Place a cut at the beginning and end of each of your sections you need to alter. After only cutting, playback will still look the same in the program monitor. However, your timeline now has several consecutive "clips" instead of one long one. Then just make whatever changes you need to to only those short problem clips. If you want to make the same exact changes to both, then just fix one and copy/paste the effects to the other.
If you need more gradual change, then you may need to keyframe the changes... don't use the razor at all; leave it as one long clip but keyframe your changes from 0% to 100% and back down, etc. where needed.