any tutorials on d space, and manipulating vertcies on different axis

I have this issue in modeling and even if I start out on a global axis the default setting and use the normal axis for manipulating my mesh in edit mode , I get dents in my mesh because of little inwards and outwards of the vertices. I did think maybe I should just straighten my vertices but that wont help on creating the shape and a good mesh since things like organic modeling and hard surfaces such as car doors that have certain bends inwards from the car floorboards to the window at the top of the door.

You probably have your proportional editing tool turned on, to turn it off/on press O.
Oh and press ctrl+N to normalize vertices, maybe that could help.