The reason that there was more than just one settlement is that it wasn't exactly the British government colonizing North America. By that, I mean that there wasn't a "Ministry of Colonizing" that sent out government-sponsored colonies.
Instead, the colonies were founded by people who were (for the most part) trying to get rich. The Crown would give charters to individuals or companies allowing them to settle some particular area. They would then try to get rich doing so.
Given that that's how they were conducting the colonization, you can see why they didn't do it all in one settlement.
As far as a Civil War goes, as soon as the South was settled in such a way as to make it more aristocratic and export-oriented (in other words, by the plantation system) and the North was settled by small farmers and artisans, the die was cast. They were too different and were always going to have different interests. It was those differences that led to the war.
You also have to remember that exactly where a ship landed was a bit of a chance undertaking. The Mayflower could have very well been aiming for Jamestown or visa vursa, after all less than 200 years before Cloumbus stumbled across what is now the Bahamas, thinking he was in China or India, not to mention "the Lost Colony" which would have been in North Carolina had it not disappeared. As for these colonies geographic positions contributing to the American Civil War, no I do not belief that a single colony would have avoided a Civil War it may have postponed it as the people would have taken longer to spread across the nation and deversify the economic and political standpoints to the extents that lead to the secession of the southern states.