I just draw 5cc into an old 12cc disposable syringe, put it i the corner of a horse's mouth and they absorb all of it. I am sure it is just as good to put it on feed; It is just easier for me to squirt it like a dewormer and go on.
I never treat topically; I just leave it alone and in a couple of weeks it is all gone and new hair growing in. I have had horses come in, especially brood mares to breed in the spring that had it all over their backs and rumps. They are completely cleared up about the same time they are ready to breed. NO horse is going to breed that is in that shape. The same lack of Vitamin A that let them get Rain Rot will keep them from having a fertile ovulation. So, when a visiting mare comes in to breed, I give her a dose of Vitamin A the day she arrives and and once a week after that until I am sure the Vitamin A in my feed can take over. It is a really cheap and effective 'fix' for a lot of things. Rain Rot is just a symptom of a greater problem, a lack of available Vitamin A in a horse's diet.