I use a lot of layer, which is not very professional, but if it works - it works.
So, about 2D and 3D thing.
There is a lot of tutorial to teach people to draw 3D space and objects, but I will used the convenient one. Not a good way to be better, but a good way if you have a perspective inept.
The trick is easy : create everything in flat objects. The object in faraway will be completely 2D and smaller and the nearer will have shadow and refection (as you see in my work) and much bigger.
Or simply using isometric which is the easiest to follow : create 3 axis of reference (x,y,z) then use it to make a 3D object.
Maybe i should do a quick tutorial about this some day...