EFT Server stores its ftp.cfg in \All Users\Application Data\. On Windows 2008, Application Data files for all users are in a hidden folder named %systemroot%\ProgramData instead of under Documents and Settings\All Users\Application Data. (You will have to unhide the folder in Windows Explorer: click Tools > Folder Options > View tab, click Show hidden files and folders, then click Apply.)
Main program files are installed in C:\Program Files\GlobalSCAPE\EFT Server or C:\Program Files\GlobalSCAPE\EFT Server Enterprise; application data is stored in C:\Documents and Settings\All Users\Application Data\GlobalSCAPE\EFT Server or C:\Documents and Settings\All Users\Application Data\GlobalSCAPE\EFT Server Enterprise.
EFT Server web files are stored in the following locations:
Resource files used to create the Web pages are stored in \contrib\EFTClient
Everything necessary for the Web site that is not contained in the resource folder is stored in \public\EFTClient
Files used by Web Services are stored in \public\EFTClient\WebServices.
When upgrading, previous files are backed up to web/backup/EFTClient
Custom files are stored in \custom\EFTClient (empty by default). The EFTClient folder in this directory contains customizations that apply to all Sites on a server. To customize files for the Site, create a directory structure in the form [SiteName]/EFTClient/ in this folder. The Site folder should hold just those files that contain customizations for that Site. The best practice is to have only customized files in this folder and to leave the original files as they were when installed in the \web\public\EFTClient folder. WTC and PTC files can be modified independently.
(For assistance editing the WTC interface, refer to Rebranding (Customizing) the Web Transfer Client.)