Don't see your problem, personally... I don't have a lot of PDF files, (and those I do have are made up for a 5" and 6" (4:3) screen, not a 7" (16:9)).
First, I put the books wherever I want them. I just moved them from my internal memory to my external SD card. No problems there. For epub, I use ezPDF (was a sale a few weeks ago) or the internal HTC PDF reader (as I can use my pen with that). They both allow me to get the PDF's from all locations, including external SD cards (though, the HTC app is rather limited as it doesn't have a shelf of any kind).
All my other books are in epub, all put on my device using Calibre. I use Mantano as reader, as I find that one the easiest to use. (Aldiko doesn't support highlighting, or at least, didn't when I was looking for a good app to use, which makes it useless to me).