Ok, so I saw this thread and it got me curious. I ran out and bought blue uchida fabric marker and did a test run on my boot. I went stitch by stitch. It took me about an hour to do the entire boot.
It is a tedious process, if anyone does this make sure you do the top of the stitch and the sides. If you get it on the other material you have about 1-2 minutes to wipe it off. I just used my fingernails to wipe if off and it came off clean. Also I talked to the people at the store when I bought it, they said it will not bleed and is nearly impossible to get off once dry.