I use Prismacolor markers to dye their bodies. Actually, the only reason I dyed Garnet (previously Sparkle Sky Rocket) was because her body had red marks on it. She had lovely hair, and I didn't want hetr to go to waste. Sapphire was a Twinkler with a bad haircut, and since I was never able to find replacement hair for her, I decided to make her similar to Garnet.
What i do with the markers is pretty messy. Be prepared to get your hands dirty. I color a patch, then I take my fingers and rub, or blend it in. This helps the color to dry faster and eliminates any marker streaks. There is a drawback though. You have to give the marker ample time to dry. We're talking days to as much or more than a week! You'll know if it is still wet, because the pony will be slightly sticky. Once it is good and dry, I run some water on it. I HAVE used mild soap on them to help remove the excessstickyness, but in some cases, it takes off too much and the color fades. I have not had any problems with them fading, but I would not advise storing them in close contact with other ponies, since the color may still transfer. I just think it looks better than painting the pony. (Not to mention I don't have the patience t put a lot of thin coats of paint on my customs...)