i can tell you that a marker on fleece will mostly get on the back of your drawing hand, and not so much on the fleece. it rubs off the fleece extremely easily.
i've read that it is easy to "write" on fleece with a sliver of soap. you might want to give that a shot. never tried it.
another thought- with scales you are going to keep repeating the pattern over and over. would it make sense to make some sort of a stencil that you could use that would go the width of your snake, then you can just move it up and keep going?
just thoughts!

best wishes with your snake. sounds fun.
-Kimberly