iPad is a device, not a format. If you're using DPS, this can't be done with the current tools.
If you're not please explain exactly what you're doing.
Finally, there is a dedicated DPS forum.
Please do not post DPS related questions in the InDesign forum.
And, if you're not using DPS, only PDF reader that I'm aware of, supports viewing videos in a PDF file on the iPad. I write about that here:
And I don't know if they support time markers. I haven't tried that.