I don't think that Book Designer is the best solution for academic files.
Stick with LaTeX but use pdflatex to create your pdf instead of making a dvi file and then a PDF.
You'll need to change de page size using something like:
Oh and increasing the font size should improve the whole thing too.
Overall, you can make something quite good looking, you'll just have to edit the paper and font size each time.
An e-ink reader with A4 and PDF support: that's what we need for academic papers !