After looking at several gengas, I notice that there's particular colors that frequently in the completed linework; blue, yellow, and red. What are they used to indicate? I assumed that yellow was used to indicate light and red was used to indicate shadow.

Blue line = shadow indicator
red line = highlight, effect

Normally, yellow is only used in genga to color some area just to make the drawing reads better.
It's rarely used for shadow/highlight markup in the inbetween drawing because it's not suitable for scanning.

Thanks for clarifying. I've been creating my roughs incorrectly.