For handgun ammunition...
When working up a load, I mark the primers to differentiate between the different powder charges. Marking is important as quantities of ammunition with different powder charges is small and getting the rounds mixed up is a real possibility.
Once I've settled on a load, I pretty much do not need to mark it. I rarely have bulk quantities of more than one or two different loads and they generally have different bullets (jacketed or JHP for the hot stuff or defense rounds, cast or plated for practice/plinking ammunition). At the range, I rarely take more than one style of this ammunition so spilling a box or bag really is not an issue as long as I do not lose the card that identifies the ammunition.
For rifle, I do similar things as handgun, but I do more testing with different bullets and powder so marking is very important to keep the ammunition separate. But, again, once I settle on a load, the do not get marked. individually.
My experience with colored Sharpies is the color fades over time and some colors look like others after they have aged. Hence, I stick with black Sharpies and use numbers, shapes, or tick marks to differentiate between different ammunition.
I do not have problems identifying different loads, but often I will load up some test ammunition and won't get to shoot it right away. Then, when I get around to doing something with it, I did not write down the intended purpose and I forget what my objective was for the new load.