Anything you don't want coloured with dye, put either white glue or acrylic paint over. Apply several thin layers and allow it to dry thoroughly before dying the pony. White glue will scrape off under hot water when you're done (so be careful with tongs in a hot pot, too) and acrylic will come off with rubbing alcohol. This works for eyes, symbols and blush. You could even do custom "blank" areas with glue or paint, where the original Pony colour would come through.
It's worked for me lots of times but I've only ever dyed G1s