It can be a big debate of charging hourly vs per project. I'm a web designer so of course my project specs will be much different than yours, so I'm not sure what is best in your case... But what I did was track my time over several client projects to come up with an average estimate to complete certain tasks.
It's tough to get an accurate estimate, but when you finally do, you realize that you come in on jobs fairly on track (within an hour or two at most). By going per project, you realize that you win some and you loose some... but it does make things simpler.
As far as the client goes, they know I'm getting X, Y and Z for $XXX. If you do a per project rate, just make sure to set the ground rules up front - for example, if I'm designing a site for someone, they'll know that for $XXX they are getting 1-3 designs, with 2-3 revisions each. If they end up requesting 5 completely different designs before they decide on one, well they know up front that it will cost extra. Just be sure to put this in your contract... I've been burned in the past - never again! LOL
If it comes to things like site updates and maintenance, etc. I do charge hourly, because that's more difficult to estimate a flat price on.
I'm an avid reader of the FreelanceSwitch blog - they've had some GREAT articles on the topic. Here are links to a few you might find interesting, below:
Hourly vs Fixed Pricing
Trading the Hourly Rate for Task Based Pay. Should You Do It?
The Subtle Effects of Pricing on the Mentality of Clients
How Much is Your Time Worth?
How to Start Charging Your Dream Rates and Get Away With It
As far as figuring out how much to charge in the first place, research of related companies can help. What's also important is to figure out how much you need to make in order to break down your hourly rate. A few more articles on that are below
Figuring Out How Much to Charge
Nine Factors to Consider when Determining Your Price
The Price is Right
Hourly Rate Calculator
LOL, I swear I don't work for FreelanceSwitch - they have just been an invaluable resource to me! Goodness, though - this would make a great link list post for my blog, LOL. Think I'm going to have to do that!
Anyway, I hope this helps a little, and Best of Luck to You!