I've used sharpies on brass without issue like everyone else.
Writing the actual numbers sounds time consuming though; I'd go with the coloured head idea. I'd get plastic boxes in two different colours (such as green MTM and blue Plano) and use one colour for each cartridge, clearly label the boxes with a marker on multiple sides, and also put a swipe of colour across the case heads as further identification. Green marker for the cartridges kept in the green MTM boxes and blue marker for the cartridges kept in the blue Plano boxes for example).
Blue and green might be too similar... maybe red and green? Opposite colours will be much more difficult to mix up than adjacent colours.