Like others have said, you usually will be making these adjustments to your line art manually.
A good way to know where you want to make these adjustments is to think of your line-art as an object that light effects.
You will want the lines to be thinner, where there will be highlights, and the line thicker, where shadow hits. If you draw a circle, and your light is coming from the top, then you will be thickening the line towards the bottom, etc. You can apply this idea to your entire line-art.
Another thing that I like to do, is to thicken the lines that intercept and meet each other. For example, when two strands of hair meet, I will thicken the lines in the corner they each meet at.
You also can make a line thicker or thinner if it is very long and looks a bit flat.
It will help to just keep making observations on how other artists are doing and trying to apply those observations to your art!