I had a scenario once, where I needed to give certain users access to multiple sub folders, without creating multiple FTP accounts. The goal was for them to see certain folders, but not others.
So let's say my folder structure is:
And my user should be able to have full control of Site1 and Site2, but not even see Site3.
To do this, first create the user, and give him only List access on the root folder
Next, add each of the sub folders he has access to, and give him appropriate access on each sub folder.
When he connects now, he will only see the folders he has access to.