While 2nd shooting for some incredible photogs in my city, I learned that bouncing flash off of the ceiling can be nice, but bouncing behind and to the side of you will produce the most attractive light. Look for white/neutral colored objects to bounce off of. However, since this is your first wedding, it may just be easier to shoot the ceiling and not have to think twice about it. I wouldn't recommend using auto ISO with flash. As you probably know, it will alter how lit your background is, so decide early on what you want and keep your ISO there (like during the reception).
As for shooting mode, I would recommend using Manual. This is where attending the rehearsal dinner will come in handy. It enables you to really dial in your settings and view it larger on your computer later that night. Since it's indoors, the lighting won't change during the ceremony... Manual will make another thing that you won't have to worry about (until the location/lighting changes). Typically, I shoot in manual when there's consistent lighting, and when we're on the move, i change to Av with +2/3 or +1 stop EC.
For my 5D3, I changed the DoF button to One-Shot/Ai-Servo. It's super handy for weddings because if you ever need servo, just reach your ring finger forward and hold down the button, then your focus will track. One thing to keep in mind, servo seems to constantly bounce a little in front and a little behind the subject, so takes a lot of extra pics when in servo to ensure you've nailed focus.