As everything in mapping, making a layout can be done in multiple ways and techniques.
Drawing a layout on a flat paper is one of those, but (as it also happens when making an architecture project) a flat floorplan will inevitably make your map have a weaker vertical gameplay, added as an afterthought.
A good layout is self-flowing (no dead-ends), three-dimensional (the game is played horizontally as much as vertically) and intertwined (meaning and the rest of the map is still present even if you change from one area to another. For example, some stairs lead you to a bridge looking over the room where you just came from)
These basic principles can also be applied in architecture, but the difference is that architects have money limits instead of r_speeds limits.
A good layout also needs different exits and escapes from each room. Players need more than one option to choose from.
Spawn and weapon placement defines gameflow and in the end will be responsible for the success of the layout.
As an example, here's a cross-section of my upcoming map, "moltengold". As you can see, the map's basic layout was thought vertically instead of on a plat plane, because there were certain objectives and desired combat situations (see the red line)
http://img71.imageshack.us/img71/1776/seccionlh0.jpg