Great articles here, especially the 2nd and 3rd:
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With a low, almost-white ceiling you can bounce the flash. If the ceiling isn't pure white it's still OK as long as it's close, and the color tint is a little warm because that color will be reflected. You wouldn't do this with a green ceiling (for example) - because you'd have a greenish color cast on the bride's face! Also, it needs to be white (or again, close to it) or it won't reflect much light. Aim the light to hit the ceiling half-way between you and the subject. This will especially help with the camera turned to vertical if you don't have a flash bracket, because it will make an even bigger difference on the shadows. With TTL flash, you shouldn't have to compensate the flash exposure, but I don't know that system. If you were using an Auto mode (not TTL) then you'd have to open up about 1-1/2 stops to compensate for the light loss and extra distance that the light has to travel. This will take experimenting to know for sure.

The top of the flash head should have a pull-out bounce card. On my older SB28, it's a thin white piece of plastic that pulls out, about 1" high x 2" wide. Use that with bounce flash for a little more "punch", which works well with the softness of bounce flash. It will also give you a catchlight in the eyes.

I'd be nervous about a "+" compensation on the flash with digital. I don't have that set-up, but highlights can easily be blown out on digital - especially on a bride's white dress.

ISO1000? I use ISO400 and f5.6 or f8. At 1000, you need very little power from the flash, but what you've got will easily handle more than the settings I use. Carry extra batteries though. Down the road you may want Nikon's additional battery pack (about $150) which will last several hundred shots and you won't have to worry about any recycle time.

Good you noted all of the directional lights - they can give you problems with flare and also throw exposure off. Matrix metering is pretty good at ignoring one bright light in a scene, but not perfect. This is turning into a book... Let me know if any other questions and I'll try to help!