Personaly, I use very fine non permanent OHP pens on both the laminated charts and the whizz wheel, black on the chart which can be read under white, red or blue light (one of the aircraft I rent has a blue interior night light) and blue on the whizz wheel (blue is easier to differentiate from the black lines printed on the wheel). Electrical contact cleaner cleans the chart and a damp tissue the wheel (dont leave it on the wheel too long).
This gives very accurate and legible markings which should be easy to measure to the standards required.
All the best for the re-take.
Nigel