I typically create something called an SOW. Statement Of Work
A document like this outlines key milestones, deliverables, and costs associated with those milestones and deliverables and the timing of payments.
I find it easier to quote as flat fees. How I do that is I estimate how many hours it will take me, multiply that by my hourly rate and generate a price. You will never get the estimation right, and general rule of thumb is that you will under estimate it so round up and include anytime for communications (phone calls, reviews, meetings).
To calculate an hourly fee, figure out how much you want to make per year. Be sure to factor in healthcare costs, rent, savings, things like that. The average work year is 2000 hours, but as a freelancer you might spend half of that time chasing work, so divide your anual desired earnings by 1000 and you should have a pretty good idea of an hourly rate.