Atrus took the time to study how the writing worked. When he read the books studied by Gehn, he studied the patterns of the words and the lines and how they affected the ages. He also studied the relationships interwoven in the lines of each book. These relationships pertained to the balance between various forces necessary to sustain life. A good illustration of these concepts can be found in Myst III: Exile, in which you explore the ages he wrote in order to teach his sons these relationships. He was very meticulous, with a desire to learn and understand, whereas Gehn was using a longhand version of copy/paste to write his books. He actually berated Atrus for taking too long in his writing, even destroying his first Age by throwing it in a fire as a punishment.
Later, Atrus' skills advanced when he was reunited with Ti'ana and Catherine. In fact, it was Ti'ana who taught him to observe carefully and to take his time in things. This was one aspect of the D'ni culture that Gehn never grasped.
"I didn't belong as a kid, and that always bothered me. If only I'd known that one day my 'differentness' would be an asset. Then my early life would have been much easier."