I use a little Oxy clean, the powder type mixed with some water to make a paste and just spot scrub it, it works very well. For the future you might want to consider using neutral polish on the inside of your boots and black on the parts that don't usually come in contact with your saddle pad. By doing that I have pretty much eliminated any black smudges on my saddle pads.
I actually haven't been using black polish on the insides! I guess my boots are just crappy and they're rubbing off the leather dye.
Thanks for the tips! I'll try the Oxyclean...I didn't know if something like that would make my pad self-destruct.
My mistake, I didn't realize when I posted that you are talking about a sheepskin pad, I never use anything but Melp, Pepede or Leather Therapy (all products especially made for hides) on sheepskin, I would never try the Oxyclean on it.