For my money, buy a pack of multicoloured permanent felt tip pens (OHP/CD pens) and just do it straight onto the chart for the areas you need to worry about only. About the time the chart starts looking seriously scruffy from this, you'll need a new one anyhow.
Don't get carried away; anything more than 30 miles from your training airfield, or 10 miles off any planned route - just ignore it.
G