I do hand quilting and for dark fabrics I use watercolor pencils. They come in every color and I can match them to the color of the fabric.
For light fabric I use a darning needle for marking (the pattern is "scratched" in the fabric and the needle tip leaves a fine crease mark).
I also tried the chaco liner and it works fine for last-minute markings that do not have to last very long. It rubs of very easily.
What I also found out is to be careful with all marking tools using yellow color - very often this is not easy to remove after the quilting is finished.
The choice of the right marking tool is always a choice of personal taste and there are many, many opportunities. Just test!