They were founded separately. North Carolina was called Albermarle and was settled by people from Virginia moving south except it was not plantation based and more farms. South Carolina was founded at Charleston many years later and developed into a plantation colony like Virginia. These differences made it hard to rule them both (plus the physical distances between the population centers) so by almost 1700 they were referred to as North and South Carolina and had almost separate governments.

You can read all about their founding in the book Conceived in Liberty which is freely available online. I am on mobile and suck at linking.

ETA: Here is the link to Conceived in Liberty. There are also full professionally read audio book chapters free for download.

http://mises.org/library/conceived-liberty-2

See Chapter 13 The Carolinas, pp 111-116.

Finally, something I can answer! I'm fairly knowledgeable about North Carolina history, as a resident of the state, so any information I impart about the Carolina colony as a whole will be biased to the North to some degree, despite it being generally less important than South Carolina during this period of history.

There were a number of figures key in overthrowing Oliver Cromwell's Commonwealth and restoring King Charles II to the throne of England. In 1663, as a reward for their help on restoring the monarchy, Charles rewarded 8 loyal nobles and key figures in the Restoration with "the land south of Virginia", which they promptly named after the King himself. While there were Virginians settling along the North Carolina coast around Albemarle, they did not really have a hand in establishing the colony. The capital at that time, Clarendon, was founded over the ruins of an attempted New Englander colony, was located at the estuary of the Cape Fear river, not far from Wilmington.

The colony split into North and South for various reasons, including differing methods of settlement - South Carolina was more densely populated, and settlers had a much easier time colonizing South Carolinian inlands thanks to flat land and traversable rivers, while North Carolinian settlers faced difficulties almost immediately in colonizing the hilly, wild, heavily forested, and generally less hospitable Piedmont region. It's important to keep in mind that North Carolina was almost completely frontier in this period. While South Carolina was ideal land for plantation farming, North Carolina was remarkably less suited and therefore developed differently economically, more heavily stressing tobacco, lumber, and tar, taking advantage of the longleaf pine forests that were so dense in the state early on.

When the administration began raising taxes and passing laws that were disadvantageous for North Carolinians, as the held the rich cotton plantations owners in the South in mind, especially those around a large settlement Northern colonists grew distant from the administration in Clarendon, fleeing farther inland into the wilderness to secure their freedom.

By the early 1700s, due to heavy taxes and a series of incompetent governors, most of Carolina's colonies had failed due to people either leaving or fleeing inland. Clarendon itself was abandoned, leaving two major settlements left on the coast - Charleston and Albemarle, which became the bases for the new North and South Carolina colonies. The division was recognized by the Lords Proprietors in 1712 and again in 1729 by the King, when the Carolinas were bought out and made royal colonies.

Interesting to note is, according to the charter, where Carolina gets "the land south of Virginia", the province of Carolina technically included Georgia among its territories. I don't know whether there were ever any serious attempts to colonize Georgia by Carolina, though.