Just in case someone is still reading after all this time....
The answer is twofold. Non-shielded, atmospheric capable ships use any possible combination (design specific) of repulser-lifts, main thrusters, (vectored and/or) maneuvering thrusters. In other-words...they use brute force for flying.
Shielded ships are not only capable of vastly higher speeds in atmosphere, but also far exceed non-shielded ship maneuverability.
As stated throughout the saga, shields themselves are adjustable for angle, strength, direction, and even shape.
A ship traveling at supersonic speeds in atmosphere, has angled and shaped its shields in such a way as to negate the simple design factor limitations of its physical shape. In short...a perfectly square cube ship equipped with sufficient shields and thrust could streak through atmosphere with no more resistance than an SR-71.
That isn't all they do in atmosphere either....
Any shape utilized would be what's called a "laminar flow". Picture it similar to a football in shape. Points on both ends with the circumference or mass of the ship filling out the larger center. With lift provided independently of shape, the actual shape of the shields can also be adjusted to behave as any given control surface.
Think of a modern B-2 stealth bomber. Flying wing.. no vertical stabilizers...yet still, it's aerodynamically stable, and still capable of pitch/yaw/roll.
Shields can abate exterior heat and friction. They can act as an infinitely adjustable control surface, and an air brake.