oh and our chapel have very low lighting. Should I be concerned if they have fast enough lenses and proper flash eqipment? One shoot with a 20D and the other might be a 5d, does the body make much difference for wedding shots?
Don't bother concerning yourself with what equipment they have...just look at their shots/portfolio. I would rather have great shots from a disposable film camera, than crappy shots from a 1Ds Mk II or a $30,000 Hassy. It would be good to get an idea of what the shooting conditions will be (dark, flash allowed or not) and let them know so that they can be prepared...but a good photographer should find this out on their own.
It's really a personal decision. You will want to set a budget and think about what kind/how much coverage you want...then look for photographers who will fit those requirements. Maybe you will want a very expensive photographer to show up for two hours to get the ceremony and formals...or maybe you want two or three shooters for all day coverage.
Do the digital negatives usually cost extra?
That depends. If they sell you the digital files...you probably wont' buy any prints from them...so I would expect there to be a significant charge for them...either upfront in the package price...or as an add on. Some photographers don't sell the files at all...some include it with all weddings...some will sell them for a price and some might include them after you have reached a certain level of print sales.
Good luck in your search and congrats on the upcoming wedding.