One of my favourite methods ... you know the Crayola washable markers? Well, they wash out of fabric too! Yes, I know - heresy!
I have not had any issues at all with the markers damaging the fabric - and the marks do wash right out. I always wash my quilts as a final step anyway.
Use the ones with a nice fine tip. Lots of colours to contrast with whatever is in your fabric.
Learned this from a LQS machine quilting class, well-respected and successful owner and teacher.