Well, modern CPU's have the integrated heat spreaders, which in theory is supposed to spread the heat away from the CPU core and over the top of the chip. While other parts of the CPU do generate heat as well, the core is what makes most of the heat and they're usually right in the middle. Now, for single core all you really gotta do is put a dot in the middle and you're good. this would probably work fine for dual core too, but quad core you'd probably want to spread it out a little more. I'd say the line method for duals and quads is more acceptable.
You could spread it out manually but thats really a waste of time, as soon as you put the heatsink down it spreads out.
But for other things like chipsets, memory chips, GPU cores, etc, the actual core is visible. On the north bridge, you look at the core...the part that makes heat. So, you want to make sure all is covered well.