Aside from the protocol (which is way beyond a forum reply), I might offer some photographic observations...
1) What camera are you using? Newer camera have very good noise charactoristics and I would be inclined to go with ISO 400 or even 800 in the church. 10D and older are not as capable in this regard. In that case I would stick at ISO 200.
2) You gear seems quite suitable. On-camera flash will produce some undesireable side shadows for vertically-oriented pictures. Most wedding pros use a flash bracket that keeps the flash well above the lens regardless of vertical/horizontal orientation. Better yet is off-camera flash for interesting facial feature modeling, but this is arduous to pull off without experience and dedication.
3) Flash for weddings is quite tricky, so don't beat yourself up if there are some flaws in the results:
- difficult to balance ambient background light using in-camera metering
- Canon auto flash exposure systems aren't all that great
- large distant groups require power flashguns
- difficult to achieve balanced lighting for multi-row and wide groups
- direct flash is unflattering
- tough to hold detail in a white dress and a black tux simutaneously
4) Available light in a dark church requires you to lurk the perimiter with a robust tripod and a loud shutter. Very hard to be subtle and move into position quickly.
5) If the reception hall has a low ceiling, try using bounce flash with a frontal fill deflector (3x5 white file card and a rubber band works well).
6) Amateurs tend to create horizontal pictures. Albums read better with verticals. Don't be afraid to turn the camera, let the scene dictate orientation.
7) There appears to be a retro movement back to delivering some of the work in B+W, especially if the composition is strong enough to stand on its own without the visual impact of color.

A lot of wedding gunners are taking a lot of diagonally oriented shots - cutesy. These will look like polyester double knit leisure suits in 20 years. A fad - IMHO.
9) Don't be afraid - your scenario is a perfect opportunity for a first wedding - no pressure!
10) You will miss some shots - expect it and learn from it. Eventually you will understand how to anticipate and miss fewer shots - no one is perfect.