Hi Aleksander -
There are a few ways to achieve what you're trying to do:
You could just put the text on the A layer only, so it will scroll up if it stretches off the screen. And if you set pinning on the box, it will adjust when the user turns the device so the top of the text is always where you want it to be.
If you left it B-layer only, you could format the text so it only fills the visible space (the square in the middle) and put some other page elements in the margin space on the sides and top/bottom. If you look at Outside Magazine, this is what they do for all their long feature stories. See images attached.
Finally it is possible to load entirely different layouts on rotation if you treat the whole page as an HTML doc. Here's our page on doing that: http://support.magplus.com/entries/21083136-new-image-on-rotate-resize-on-rotate