When I adjust the parameters on my scanner to compensate for any color issues is that actually changing the way the negatives are being scanned or is it just applying these changes in "post"? I hope I articulated my question correctly. What I am trying to ask is if I should re-scan the pictures with modified settings or should I edit the already scanned pictures in Lightroom.
It depends.
Some software/setting choices at the scanning stage can leave you with a file that is difficult to correct back to normal with post-processing choices available in something like Lightroom.
Think, for example, of a file that reveals an image that is way too dark or way too light.
It would be a good idea to experiment with some re-scanning. Try some scanning adjustments, and note the ones that seem to give more pleasing results. The settings used for those may be ones that you will want to use as your new "normal". Depending on your software, you may be able to incorporate those adjustments into a custom profile for that combination - that film developed with that kit.
The thing to be careful of is using an unusual scene to base your "standard" profile on.
I picked the shot I did because, if it is exposed normally, that negative might be a reasonable one to work with - fairly normal lighting and reasonably typical colours and tones. Some of your other shots may be more unusual, and as such may be more likely to confuse any "automatic" functions in your scanner and software.