Forget about the terminology for a second.
If you want to get a general understanding of circuit design, think about it in terms of connecting points. The London tube network is a good analogy for this. When starting out designing a circuit, you think only of which points need to be joined together. This is similar to the simplified tube map that many people are familiar with:
http://www.bbc.co.uk/london/travel/downloads/tube_map.html
However, that map only represents a simplified version. The real geographical map looks more like this (this is still simplified as it doesn't show information about the height/depth of the tracks):
http://www.tubemapcentral.com/mythset/geomap.jpg
It's the same with circuit design. You start off with a simplified version, but the physical version is frequently more complicated because you have to work over multiple 'layers' in order to stop wires that cross over each other that shouldn't be connected from touching each other. That's where things like 'vias' come into play (vias are the points at which layers of a circuit board are connected to each other).