That's quite a responsibility they've heaped on you!
First, and foremost, practice shooting in the conditions you will experience during the wedding. Practice your manual exposure and focus controls until they are second nature.
The reason manual controls are preferred is because a light or dark background, etc. can throw off your camera's automatic exposure controls. Same with focus - when shooting two heads, one is usually to each side, allowing that picture or window in the background that is between them, to grab focus away from your subjects.
Auto-focus and auto-exposure should be called, "random-focus" and "random-exposure".
Next, use a tripod. Whenever shooting a stationary subject where the camera will also be stationary - especially if more than a few seconds, you need a tripod, not a monopod, not a stabilizer, but a tripod.
Decide on the style of wedding video you'll be producing. A single camera shoot is best suited for a stylistic (short form) wedding video, but even these should strive to capture the vows clearly. Best way to do this is by miking both groom and minister with wireless lav mics. If this isn't possible, try to at least get a digital voice recorder in the groom's jacket pocket and clip the lav mic to his lapel, about where the two sides come together, or wherever needed to have an equal distance from both groom and bride's lips.
Since you'll likely be using just one camera, you won't be able to use the triangle camera positions of a three camera shoot. Therefore, you'll likely be toward the rear of the church, or as far forward as they will allow you to be. If so, ask the officiant to position the couple so they are facing one another with the officiant behind and between them. This gives you (and guests) the best view of everyone.
Be aware of the photographer. Many photogs feel it is their duty to position their backsides right in front of the videographer's lens! X-D
We can't really write a "how to manual" in a forum post, so be aware that any info you get here is barely scratching the surface. Try the Search feature of these forums for keyword "wedding" - you'll turn up a lot more info.
There is no way you'll do a great, professional job on your first wedding shoot. No one ever does, so go easy on yourself and realize that this is a learning experience. Have fun!