Michael,
Go with track planning software. Its easy to do slight variations to the plan without losing the original. I must have hundreds of saved files for my current layout build, each one having a slight change to see what happens to the overall design. If I didn't like the change to the plan then I would go back to the previous saved version to try something else. If after doing many changes to get something I wanted but it didn't work out, I would go back many versions and start over from there.
My pencils, graph paper, track templates and erasers are in a drawer somewhere; haven't used them in years.