When I work with brushables, I usually have used ones that already have the hair I want. Since I handpaint, I separate out the head and body (easier to work with that way, since there's only one section of hair on each) and braid the tail and main, then secure them. If it helps, you might consider braiding them wet to help with any strands of hair. Then you be vewy, vewy careful around the areas with hair. I usually leave them for last and only approach them from one angle at a time, then let it dry, then go to the next angle, etc. For in between the plugs, I'd suggest not going through all the way, just do the top of the head and the bottom. Get the pony's hair wet, separate it out so that you have two lines of hair and a clear strip down the middle. Then put an elastic or something securing the two lines of hair together under the pony's head.
Someday, I'll get good at re-hairing...