Do you already know the general contractor that you would like to build your house? If not, it would be a good idea to interview a few different ones. You could look up their information with the local Association of Builders, ask how long they've had their license, how many houses they build per year, and if they have any references or past clients that you could call. It is of utmost importance to choose contractors by their reputation, not by their price! Also, make sure you know their warranty policy. They are required by the state to provide at least a one-year warranty.
Normally builders want to make about 20-25% of the total cost of construction. If you already have a floorplan, the builder could give you a general idea of what it would cost per sq ft to build, then add his fee onto that, plus the cost of the lot. What you could do is get the estimate from the builder and compare that with what similar houses in the same area are selling for, and decide that way which route would be best.
One other thing to think about is financing. Banks have tightened the guildelines across the board, but they have really tightened up in respect to new construction loans. I believe that most all construction loans now require 20% down plus an excellent credit score. The builder also has to be approved by the lender. It would be worth your while to talk to a morgage broker about your options an expectations before you go much further.
Hope this helped! Good luck!
Keller Williams Realty of Greensboro