Don't agonize over the question if two items are related and how they are related. If in doubt, just connect them with a dotted line or a line with pale color.
The easiest way to distinguish larger towns from smaller villages on a map is to color them red. So if I identify a major concept on my map, I use red, too. To indicate [dis]agreement with red and green, has not proven universally useful. If a lesser hierarchy ls needed, I often use orange, for higher levels (rarely) purple.
More about colors see in Optics.