If I'm reading your question correctly - if/once you learn a song, then as you refer to a chart you will know whether the scale degree is higher or lower as you're playing it.
For initially charting out a song, I use my own system of writing down a little "L" (maybe/maybe not in parenthesis) underneath the scale degree so I'll know if it's intended to go below. If it's not there, I go higher. Any type of code can work since you're the one writing it out, i.e., maybe a little line underneath to signify "lower". Sometimes, it doesn't matter since as I'm playing a song, maybe I'll change it up for effect and go lower when I usually go higher, or vice versa, since it's the same pitch. Of course, if you're then going to hand your chart to someone else, they won't know what your little Malcolm Code means until you explain it to them.
It's been a while, but iirc Ed Friedland's Complete Bass Method book may have done something similar to differentiate higher/lower. That's probably where I "borrowed" the idea from.