1. Write in the stop numbers.
2. Write in the shortenings of stop names.
The problem with the first method is that you don't know what exactly stops to change, you only see the numbers. Also if you want to re-use the same composition on a different organ, you have to erase or remove every registration marking to fit the new organ. And if you play the same piece after a break of several years, you might even not remember what stops did you use.
The problem with the second method is that it takes time to get used to such system (for example, instead of adding Principal 8' and Subbass 16' of the pedal division, write Ped. + P8, SB16 etc.). But the beauty of this method is that it allows you to see what stops you are using.
This method prevents strange mistakes an assistant can make. For example, instead of pulling 37 (Mixture), would engage 38 (Trompete). If you knew the difference between the Mixture and the Trompete and had at least a partial sense of good taste, you wouldn't get confused, right?
Sure, it's easier for the assistant (and for you) to only worry about the numbers but in the long run, it's far more effective to actually help both of you think about the stops themselves.
It's better to use your brain in addition to your eyes.