Since 2010, when I began freelancing, I have discovered that the best way to charge for my services is per hour, rather than per word. Obviously, the more complex the job, the longer it will take, so proofreading a 200-page book will cost a lot less than editing it.
I charge $60 per hour. Once a client has expressed interest in retaining my services, I will do a sample edit so that I can give an estimate as to the likely final cost of the project. I will continue to update the client as the project progresses so they are kept aware of the cost. So far, I've been on target with my estimates.
A full, developmental line edit of an average-length novel will probably take anywhere between 60 to 90 hours. One manuscript review I did recently took me 16 hours, including reading, write-up, and discussion with the author, but another, much shorter manuscript took only 6. A recent proofread took 21 hours.
A writing project will obviously take a lot longer than any kind of edit. I can only give estimates as to cost once I have detailed information about the nature of the project.
Once I have agreed to a project with a client, and I've given an estimate of the likely fee, I expect a quarter of the fee up-front, another quarter when I am halfway through the edit, and the rest when I deliver the manuscript.