If you are having a hella time trying to get your FTP program to find and use an alias to a directory on a server, you are trying to use the alias in the wrong way. What you are looking to do is mount a directory and bind it to another directory.
The Problem
Say you have shell (SSH) access to a server. Logging in (scp username@server_address) you are taken to your personal user folder on that server (say "/home/johnvsc").