I just found this program today and so far it is great! I used to do all this manually, converting size, flipping double pages, and converting to PDF for my Nook.
This makes it so much simpler and saves me a lot of time.
I have one suggestion for the program I have not seen or been able to find. Choosing my own output directory so that I can separate the files and not have to pick them out of the main input would be very nice.