Gimp can sometimes be really difficult and tedious to work with, especially when creating white markings, and the method you use really just depends on you as an artist and the stock you are using.
One of the best methods to add markings on a horse is to select the areas you want to change the colour of, and then go to the Colours/Colors heading in the top menu bar and basically play with all the settings the come under it. Eg. Brightness-Contrast, Hue-Saturation, Colour balance... A good general way to begin making white markings it to turn the brightness most of the way up, and the Contrast up just a little (works for me).
It may also be a good idea to desaturate the areas of the horse where you want to add markings before hand.
(Premium and Brindle beat me to this one)
Another way to create markings is to paint over the selected areas (on a separate layer) with the colour of your markings, and then change the layer mode to soft light, hard light, overlay, hue or whatever one works the best for you. You may also need to play with the opacity of the layer, and again, destaureting the horse layer before hand may come in handy.
Hopefully this all makes sense and helps you out, if you would like me to go into more detail then feel free to pm me or just let me know in this thread ;).