I think any kind of a marker that will hold up would be fine. I do think I'd try to practice on the exact fabric I want to mark on. It is my experience that markers move differently on different fabric and it would be good to get a feel of it.
I'm curious why the stem stitch is giving you trouble. It is a very easy stitch if you have good instructions. Here is a nice little video if you ever want to give it another try.
http://www.needlenthread.com/2006/10...rial-stem.html