The most significant difference between the Northern and Southern Carolina settlements was that

The southern settlement grew rich on rice while poorer farmers in the north grew tobacco

Explanation:

North Carolina Colony was mostly run by agriculture and tobacco was its main product. The main cities of North Carolina developed around the largest tobacco companies. At the same time, South Carolina was also based on agriculture, but its main product was rice.

The most significant difference between the Northern and Southern Carolina settlements was that southerners grew rich on rice while the northerners poor grew tobacco.