Convert to epub
I hope I understand your question correctly. Kovid will no doubt respond as well, but it quite early here in the States.
Highlight the line showing the book title and author and press the convert E books button. Make sure the drop down box in the upper right shows epub and press ok.
Then the book will be converted. Next I press save the book to disk button so I can locate it easily to transfer it to my mobile device. You can transfer the file directly using the send to device button.
Since I had the Sony software before I had calibre, I use the Sony software to transfer the book(s) to my 505, but that is just a personal habit.