I don't use dropsync, so I don't know the workings of that. On my reader I have the settings set to download books to the sd card. But usually if I have books I've downloaded to my pc I plug my Reader to the pc, touch the Data Transfer button on the reader when it recognizes the pc then I go to START->COMPUTER->(F
(or whatever drive it sees the sd card as. It should pop up as 3 different drives, one is Sony Reader, one is Software, one is the sd drive. I drag files to the Downloads folder on the sd card. Disconnect the reader from the pc.Once I'm done and press the home screen on the reader and it will put the new books in the Recently Added section of the page.
Method two involves me using dropbox. I drag the books I want to my dropbox "epub" folder. I turn on my reader and connect to the internet and go to
http://www.dropbox.com (I have the epub folder bookmarked on the sony browser). I make sure I refresh the page (because sometimes it doesn't sync right away. Then I look at the dates to find the newest stuff I uploaded to dropbox. Once I find the title, I take the stylus and hold it on the link and gives me the options of Opening the link or Saving the link. I choose Save link and it downloads the files to the Sony Downloads folder. Once I'm done and press the home screen it will put the new books in the Recently Added section of the page.
Although since you are talking mediascanner app, I'm guessing you are rooted then huh? So I don't know if any of this will help you at all.