Symbolism, Imagery, Allegory
As you might expect in a novel where the supernatural takes center stage, images of darkness and light are everywhere. We get a good sense of how darkness and light are valued in this world when Merlin's grandpa complains about his coloring:
"Six years old this month, grown like a weed, and no more like any of us than a damned devil's whelp would be. Black hair, black eyes, and as scared of cold iron as a changeling from the hollow hills…" (I.1.18)
For Gramps, light hair and light eyes = good, one of us; but dark hair and dark eyes = demon-seed. It's a superficial way of determining moral or spiritual goodness, but it's an age-old way of doing it, we're afraid.
Both Ambrosius and Merlin benefit from a sneaky use of light imagery to prove their goodness or worth. Niniane names her son secretly after his father, whose name also literally means "light":
"Emrys, she called you. Child of the Light. Of the immortals. Divine. You knew that's what it meant?
[…]
"Ambrosius, prince of light. […] She told everyone that my father was the prince of darkness. I've even heard a song about it." (II.12.94, 101)
It's an easy way for us to know which characters are the good guys and which are the bad ones. It also works in terms of religions. Ambrosius and Uther are devotees of Mithras, god of light; Belasius, on the other hand, is a druid—a member of an illegal religion that operates in the darkness. Ambrosius explains why Uther hates druids so darn much: "Uther has no love for them. He is one of Mithras' fanatics, and light is the enemy of darkness, I suppose." (II.12.24).
Light also symbolizes knowledge and understanding. So it's no accident that Merlin can only see the future when he's gazing into a fire or some other light source. Knowledge itself, like physical light, is a good in and of itself. Merlin promises that the pursuit of even the slightest morsel of either is a worthy life goal:
"[…] what I am looking for, you have to look in strange places. Men can never look at the sun, except downwards, at his reflection in things of earth. If he is reflected in a dirty puddle, he is still the sun. There is nowhere I will not look, to find him." (II.12.93)
Merlin sees anything that gives light as a blessing, especially in the darkness of life in a violent place like Britain. So it's no surprise that he sets Stonehenge up to be a magnifier of light (read: goodness, life, revelation) over the grave of his father.
It's his way of saying that the good guys will always prevail.