I have done quilts for a couple of friends, and I KNOW that I did not charge enough. On one of them I just gave a total.
If I were to do it again, I believe I would charge by the hour. Make it understood, up front, that you value your time. Maybe get the details in writing. (That might sound a bit tough, but you have to be fair to yourself) I have been burned a few times and now I am very wary.