1. Just go to the "Free Apps" tab at kobobooks.com, and click "Mac/PC" at the bottom. Or go straight there:
http://www.kobobooks.com/desktop
2. I disinfect, then use Calibre.
edited to add: Is there any particular reason, though, that you're trying to use the Kobo desktop reader? I find the best way to manage ebooks on my iPad is just to use iTunes/iBooks, or Stanza. I don't read ebooks on my Mac, though, so I don't know what the advantages and disadvantages are of the many different software options for that. Just wondering why Kobo in particular, for you, given that you don't have a Kobo reader.