After they were all colored, I set them in the open window for a couple hours to get the stink out. So far, the color's rubbed off on the laces a bit, and I haven't worn them in the rain yet, but I have a feeling the color won't run too much. Just be sure to not wear your favorite socks the first time :)
The best part is, this process will work great on pretty much any kind of shoe, just make sure to give them enough time to dry.
What color would you make your shoes?