I've done it both ways. I have a program that allows you to make charts, but I find a pencil and graph paper easier, somehow--I don't have to work within the confines of the computer's symbols and can make up ones that are meaningful to me.
I just go from right to left on the chart, pencil in hand, and use one box for each stitch. For stockinette I leave the boxes blank, and I know that the front in knit and the back in purled. For cables I draw a slash over the number of stitches it takes in the direction the cable will go. YO's are a circle, and if there is a part that has a variety of knits and purls, I write k and p in the boxes.
Any other decreases or increases, I either use a symbol that other charts have used or make up one that's relevant to me and make a little key.
The thing to remember, though is that when you chart out something like a k2tog, you put that symbol in one box, since you chart what you end up with, not what you used to get there.
That's why a yo has it's own box, even though it doesn't use a stitch. Even a double or triple decreases ends up with one stitch, so the symbol takes up one box.