HI! It's fun customizing ponies and figures, especially if they come out the way you envision, right? ^.~
I remove the cutie marks with tea tree oil (it's perfectly safe for them, and comes off super easily!), and then rinse/dry.
After the pony is dry, I use diluted acrylic paint and apply it with a super fine artist brush. At least 10/0 size or smaller.
You can use any acrylic (as long as you dilute it to the consistency of cream or milk) for a good effect, but the best, longest lasting is Liquitex brand.
Good luck and have fun!!