There are really only two things you need to remember about network operations :
1. You won't be able to hide folders on a network drive unless Magic Folders is installed on the computer that hosts that drive.
You will need to ask the Master Account holder (the person who installed Magic Folders on that computer) to create an account for you. You can then access your account using the password they give you and change your password to something only you know. If you do this, the Master Account will not be able to view your hidden files or know what they are - unless they uninstall, in which case all accounts' hidden folders become visible.
Likewise, if one or more of your local drives are shared on the network then you (or whoever installed Magic Folders on your machine) can make accounts for others to use when accessing your drive(s).
2. In order to hide files on a network drive the drive must be mapped to a local drive.
If the mapped local drive doesn't show up in Magic Folders then close Magic Folders and use Explorer or some other program to access the network drive and then restart Magic Folders. Sometimes Magic Folders won't see the mapped drive unless it's been used.