The short answer is yes. If you point the User Search Base at the top level domain, then a search should include all containers and uses under that domain.
You always need to start out running the AD plugin against the Schema master in the top level domain, in order to make the necessary schema changes in AD. After this is completed, you may re-run the AD Plugin at any time, to point the Search Base toward whatever Users container you choose. This is necessary only if your Search base is going to be different than your Creation base. If you have users dispersed in different User containers, then you will need to point the User Search Base to the least common OU. . . or in some cases, to include all users, it may be simply the top level domain.