Yes, you need to create a Site (Site collection) and configure the permissions accordingly. Designing the structure depends on many factors, and without knowing anything about your current environment, no one can give you anything more than generic remarks. That said, there are multiple articles out there discussing the process and tools to use in such migration. Most of the tools support permission mapping as well.
Generally speaking, people will "add" content by clicking the Sync button on a given site/library. If you dump everything in a single location, they can select from the tree-view control, much like browsing a folder tree. But you should not aim to "sell" them OneDrive as a replacement for file shares and such.
