How does one reorganize one's entire Aperture library from scratch?
Solution 1:
By default, there is not any magic when importing photos to aperture.
Probably at that point, what it might be confusing is that Aperture has transformed your iPhoto albums to folders/projects, which are not what you exactly want.
My advise would be to create one project, move all your images there, delete all other projects/folders, and then create new projects as desired.
Furthermore, you can find a lot of articles of how you may use projects/folders to organize your photographs, like this one.