You don't necessarily need to aim for flat negatives, that may mean you can't print them properly another time in a darkroom, but if you are scanning the contrast should really be adjusted in post processing. So when scanning you should aim for a flat tone image, where you get all the tones and there is no clipping of either highlights or shadows. It will look horrible, and nothing like the end result. You then adjust it all in Lightroom or Photoshop to achieve the contrast and range you want. It is a big waste of time trying to get anywhere near the finished image at the scanning stage because scanning software is too crude. Additionally a flat 'master' image is open to further options being explored because it maintains as much information as the scanner can give, so you can start again and try the picture a different way, a bit like trying a different paper grade.
Originally Posted by powasky
In relation to your question the negatives contrast is achieved by exposure and development, what you are doing with say a yellow filter is adjusting the tone of areas within the picture. So a blue sky maintains the separation of tonal values when otherwise it would render nearly as pale as the clouds etc.