When you have multiple folders for users on Filezilla server, the only folder that show up is the home folder. Follow the procedure below to make other folders show up as well.
When you go to users folder you will see folders you created but the one with H (c:\FTP) will show up when user logs in to their ftp server.
Right click on the folder you want to make available and select Edit Aliases. Put the aliases you want to appear on the users folder. In the example below, the folder will show up as the directory under the home FTP folder when the user logs in.