You don't need to put your elements
in the install directories for PSE or the Organizer. I'd recommend that you have a directory that's just for elements somewhere on your computer (under "my documents" or else where). Once you have all the elements unzipped in this directory I'd suggest bringing them into the Organizer and getting them tagged before you start working with them. I just say this because I know that if I don't do this right away I tend to forget to get them in the Organizer for a long time
Check out this
tutorial for the basics of using the Organizer.
Most elements should NOT have a white background that you have to remove. When designers create tags or any element with a hole or transparent area to it, they save the files as PNG files. PNG allow for transparent areas in the image. Most background papers will come as JPG files.
HTH! Please holler if you have more questions.