Hey, that looks great!
For marking, I use a metallic silver colored Sharpie. It shows up well and is durable. Most of my marks end up inside a hem, but I don't sweat it if they are visible in the final product as I'm shooting for function, not form.
A trick I've learned for stretchy fabrics, is to make a mark every foot on both pieces. As I sew, I make sure that the marks stay lined up. My machine likes to pull the lower fabric through faster than the top, and these marks help me make adjustments.
Enjoy that nice warm quilt this winter!
"Life is a Project!"