You won't be able to directly load a book with the card in the eBookwise. You'll need to wait for your card reader to arrive and export the book to the card while it's plugged into the card reader.
The card reader will show up in My Computer as a removable drive, in my case it's drive G: so my path is G:\ebooks
Sorry for giving you the impression that it would work in the eBookwise itself.
Please be aware that the SmartMedia cards are electrically fragile. DO NOT INSERT or REMOVE the card with the reader on. It can damage the eBookwise and/or the card. I have folded a small piece of tape over the edge of my card to make a little tab or handle that makes getting the card out of the eBookwise much easier.
You may want to read up on Nick's impserve, you may be able to load books directly onto the eBookwise with out it being registered.
Check out this thread (it's a sticky at the top of this sub-forum), http://www.mobileread.com/forums/showthread.php?t=28363