im new at this too and ive learned that for the horizontal and vertical views you have to have two files in your folio, one that is ends in _h and one thats in _v . all of your folios have to have a vertical and horizontal option or else it wont work, you cant mix dual orientation with single.
You should ask questions relative to creating folio files to the Adobe Digital Publishing Suite Forum:
There are severe limitations to using PDF files on iPads because the PDF readers are very immature. Most of the applications don't support interactivity. Here are two postings I did on PDF readers:
EPUB files currently only support Latin languages. When I did an EPUB file that used Sanskrit, I had to rasterize the language (it was only short sections). InDesign CS5.5 or CS6 would let you choose the image resolution up to 300 ppi. Of course, you could then not interact with the text because it would be a picture.