Can you add directories and files in the home directory?
Yes, as many as you want.
Also, if you add FTP users, can their access be limited to the specific domain directory, such as /home/username/domain2.com/, or will they have access to the home directory as well?
No. Each user is equal, which means that if you add user2 to your account, her home directory will be /home/user2
If you give her control over one of your sites via the control panel, the filesystem path to this site's directory will be /home/user2/(sub.)example.org
If you want to share a site with this user, with both of you having access to all the files in a given site, you can set group permissions via SSH.
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