Stephanie, the best way to do that is to figure out how much you need to make an hour (to pay yourself, taxes, marketing exp, rent etc) and then estimate how long to convert a manuscript to an ebook, including all versions and all proofing rounds.
Easy! ;-)
Seriously, for freelance ebook designers, there is no flat rate. You can’t compete against online services that advertise “50 cents a page” or “$149.00” etc. You sell your own expertise and attention to detail, then price the job accordingly.
My design firm (senecadesign.com) does ebook design and conversions, and our fees have ranged from $350 to $4500 for one ebook (the latter was a monster project with 6 months of major revisions). Always ask for a sample of the manuscript (Word, PDF, or ID file) before you give a quote estimate, too. This I’ve learned the hard way. ;-)
AM