I often don't know what the quilting will be until after the sandwich is made. I have used a lot of methods to mark, and sometimes I just wing it and don't use any markings. Last fall I hung a Carpenter's Square quilt in the closet waiting to decide how to quilt it. I still haven't decided, so it's still there.
I have found a great way to get rid of colored chalk lines. I bought the vacuum attachment for cleaning sewing machines, computers, etc. The brush attachment with a little scrubbing motion gets rid of the unwanted chalk.