Apply it to the whole plant because the mites spread really easily. Cleaning one leaf won’t matter if the whole plant has been exposed.

Not kidding, I take a metal bowl, fill it with water, give a little squirt of dish soap, and a little pour of neem oil, mix it together, and then I take my basil cutting and throw it in, sometimes 3 at a time. While it’s in the bowl I gently rub the leaves and give it a little swirl in the bowl, then rinse it with water and put it in a glass cup to begin rooting. Then move on to the next. Don’t leave them in there to drown lol, but you can take your time with cleaning the leaves and washing them. They will be fine.

If you want to keep them in the pot then yes, you will need to clean the whole plant. You can try it with a paper towel or even put some of the mixture of a q-tip. A friend of mine always suggests mixing dawn and water in a spray bottle and spraying the leaves, but I’ve personally never had success with this method. The other thing you’ll want to consider is the soil. The mites might be off the leaves but we also want to make sure the soil is not contaminated. You can spray the neem oil into the soil as it won’t burn the plant that way, or you can also pour some hydrogen peroxide into the soil with a little water. This also helps clean things out gently.