What do you mean by theme? It is usually a list with links in it. All platforms should honor the toc specified in the ncx and opf. They need to be identical if I recall correctly.
Of course it is possible to have a page that is not listed. Just don't specify the link and it will not be visible in the toc. In Sigil you don't really have to worry about the TOC. Just make sure your chapters are specified as headers and the TOC is automatically build. If you don't want a certain chapter to be visible in the TOC, you can deselect it in the TOC editor.
If you want to do this by hand, take a look at
Jedisaber site. That explains the format rather good and helps you create an epub by hand.
The last part I don't get. What do you mean with left and right page? What reader are you talking about? I am afraid that you refer to the awful iBooks... In any case I don't think it is possible. For more iBook quirks, see the book by Liz Castro. She mentions most things Apple did not get right and how to work around it.