What I do is to upload my photos from the camera's CF card to the computer through a CF card reader (there are also multi-memory card readers available to cover SD, XD, whatever, cards, too). I upload to a new file that I set up on the desktop, and then from there I copy to another HD before doing anything else. After that, I open Photo Mechanic and review all the images, kicking out the bad ones, etc., and set aside good ones to then be imported into Aperture. I post-process in Aperture and then from there ship the images to Smugmug or Zenfolio.
I don't use iPhoto except to upload images from my iPhone, so am not familiar enough with it to tell you whether or not there is some way you can designate "private" folders. I would think that rather than showing people your iPhoto files directly on your own computer you could take/send them to a website/photo hosting site and there, indeed, you can make certain folders private.