1 and 2.) If you need both a horizontal and a vertical, or multiple sizes, you would need to create different EPUB3 files. There is no ability to adapt the layout: It is fixed (which is why it's called Fixed Layout).
If you want adaptable EPUB, you choose the other alternative.
3) In InDesign, choose Object > Insert HTML. Paste your HTML into the empty field.
I don't think this is what you meant, but it's a start:
You can edit one line in the OPF file of a fixed layout epub to make it rotate properly when you switch from horiz to vert orientations. I think Adobe forgot to add this as an option, and expect them to fix it soon.
It does *not* reflow the content — as Steve said, it's fixed. But it lets people read the epub in whatever orientation they feel most comfortable with.
I demo the problem and show the solution in this movie from my lynda com title:
To cut to the chase, unzip the epub, open the content.opf file and change this line:
<meta property:"rendition-orientation">landscape</meta> [or it might be "portrait" instead of "landscape" -- AM]