To publish an application using the FTP feature in WebMatrix, please refer to these instructions:
Click the lower portion of the Publish button, then click Settings
Select FTP from the Protocol drop down menu
Server Name: use your secondary FTP address (ftp.yourdomain.com)
Site Path: leave it blank to default to the www root folder
Username: FTP username
Password: FTP password
Destination URL: make sure this is in proper URL format. For Example: http://myDomain.com or http://myDomain.com/folder2
Click Save to save your settings and you can now publish using WebMatrix Publish button.