Well personally I think it’s a lot better to not be in that situation to begin with, but if you have a seedling or very small plant in a big pot I think it’s best to water the entire pot. It will be a longer wait until you can water again, but at least the roots won’t be running into dry medium.
If you currently have autos in solo cups, here’s a link to my journal. I grow autos, and always start in cups and then transplant once into the final pots. A good amount of what you need to know is in my journal.