I don't know how things work in Nikon World but in Canon land, when you use flash (or even if you don't) manual exposure is recommended for the camera, trying to get an exposure that brings the ambient light up to almost a full exposure, or maybe 1 stop below. You then use the flash in TTL mode, fairly lightly, just to top off the ambient exposure and fill shadows in the eyes and add a catchlight.
Avoid direct flash if at all possible. Find a neutral surface to bounce off, so you have soft lighting and not harsh flat lighting straight into the face. Ideally, flash should be used for creative lighting enhancement, not as the main lighting.
Even without flash, manual exposure is a good plan. You don't want to be fighting your exposure compensation every time you grab a lensful of black tux or a lensful of white dress. Ditto if you zoom out and get loads of backlighting from a window vs zooming in and having the window vanish from the frame.
Above all, shoot raw. It will give you more latitude to fix exposure errors or compensate for difficult light, even if your exposure is as good as you could hope. It will also let you sort out WB after the shoot and not be concerned about getting it perfect from one shot to the next.
I don't really agree with the carpet bombing approach. I shoot around 600-900 shots at a wedding, as a second shooter, and cull that to around 250 or so. The more shots you have the more you fill your cards, the more you wear out your flash batteries and the more rubbish you have to wade through afterwards to find the shots worth keeping. Less is more! Concentrate instead on checking your histogram for good exposures and picking your moments for a good capture, with nice expressions etc.. Shooting anything that moves is not the answer.
On the subject of anything that moves, don't forget things that don't move. Details are nice to get - bridal bouquet, details on the dress, table decorations, place settings, champagne glasses, rings, cake etc etc. Try to get at least one good portrait type shot (not posed, candid is perfect) of individuals or couples throughout the day, relaxed and enjoying the occasion. Have a look at the "Wedding 4" link in my sig for some ideas on grabbing candids.
I shoot with two cameras and have a 17-200 f/2.8 IS lens on one and a 70-200 f/2.8 IS lens on the other. Both have a 580EX flash mounted, but I try to avoid using them if possible or have the FEC dialed down for a subtle effect. Most of the time, especially indoors, I am stuck on f/2.8 and will be at either 800 or 1600 ISO for the indoor shots. That's the reality of wedding photography. You need fast glass and high ISOs.
Feel free to ask specific questions if you have any, but remember I am a Canon guy so can't help with the foibles of Nikon gear. Oh, and I've only shot four weddings so I am hardly the oracle on the subject, just trying to help
EDIT : p.s. I shot my first wedding (Wedding 1 in my sig) two years ago, just 3 months after I got my first DSLR and days after I got my 580EX. I only had one lens - the painfully slow (aperturewise) 17-85. I made a monstrous hash of the shoot, using Av mode (Mistake!) and getting big problems with exposures, subject blur and white balance. The blurred shots had to go, but the exposure and WB problems could be fixed fairly well as I shot in raw. I shot 622 images that day, from 07:00 to 21:00, and ended up with ~160 keepers. The B&G loved them
