Calibre is the way to go. I format all my books for the Jetbook in epub because the page formating and the zooming of the Jetbook make that the best format.
I no longer plug in the port of my Jetbook it is just too slow being it is a USB 1.1 version.
I purchased two four gig SDHC cards for use with my reader. I have the interface for these cards built into my system and allow Calibre to copy to disk for loading the books.
Please make sure you ad or remove the SDHC card from your Jetbook with power on so the system recognizes the card has been changed. This will make sure your Jetbook sees the changes on the card.
I use the internal memory of the Jetbook to hold the books or references that I always want on my Jetbook. The Bible, reference manuals, etc....
Welcome to the club, I find I now do not go anywhere without my Jetbook and it seems I am less frustrated having to wait somewhere because I can just turn on the Jetbook and fill the time with filling my mind.