Why are you not setting up the master page properly? Create a primary text frame.
What D you mean with ebook?
ePub has no exact size predefined by the layouter it is like xhtml.
PDF for screen (Export PDF with interactivity) is exactly so as you design it.
I've not been using Master Pages.
I'm using Indesign to create an ebook which I will output an epub file.
I set the page dimensions then I have been adding a page as I progress and then using the Type Tool to create a text box for each new page.
So when you say 'ePub has no exact size predefined by the layouter it is like xhtml.' does this mean the text box size doesn't matter?
That’s what it means. EPUBs are free flowing and based on HTML/CSS not a fixed page size.
The text size box doesn't mean nothing in epub. But some of the text frame settings are, like maximum column width.
But you should consider to use master pages for setting up pages, but also styles (Paragraph, Character, Object, Table, Cell). I suppose you are not using them at the moment. And you should also define the tag export section in the styles where it is available at the moment (paragraph and character.)
If you need to publish to epub you should also get some basic konowledge of html and xhtml.