As far as organizing files with BeBook, only the book title is displayed for Mobipocket files (as per metadata contained within the file itself), and folders are probably the easiest way to organize (e.g. Author>>Series>>prc files).
For storage, the largest size is 4gb (see specifications
here, and I suspect the card must be SD (and
not SDHC).
I don't use my BeBook for audio books or mp3 so can't help you with battery life, I'm afraid.