Even for bike shops, fitting a bike is half science, half art. For the rest of us -- who usually have only one or two bikes and no backroom full of spare parts -- it's mostly art. Even voodoo, until you realize that a bike setup involves honing several variables at once.
Here's a few links that take some of the voodoo out of it. I've been researching this, in trying to build up a new bike for my wife. There's lots of words of wisdom here, and it will give you some knowledge you can bring into the shop. In general, fitting is a series of compromises, since bikes are built in incremental sizes, and people aren't. It seems that bike fit is usually a bigger problem for women, since (until recently, at least) most manufacturers built frames based on men's proportions.
Some of these articles are long, and address choosing frame size. This probably doesn't apply to you, unless you missed the mark wildly on choosing a frame. But they all talk about things you can change: stem length, handlebar height, seat height/angle, crank length, etc.
Good links here:
http://www.myra-simon.com/bike/tips.html (especially the "Bodge Your Bike to Fit" link)
http://www.blayleys.com/articles/womensfit/
http://www.coachcarl.com/training_articles/bike_fit.htm
http://www.prodigalchild.net/Bicycle6.htm
http://www.sheldonbrown.com/frame-sizing.html
http://www.peterwhitecycles.com/fitting.htm
http://www.nettally.com/palmk/BikeFit.html
A couple others that might be helpful:
http://www.myra-simon.com/myra/bike/cranks.html
http://www.cptips.com/bkefit.htm
These all helped greatly in setting up my wife's bike. Happy reading!
-- Mark