I have had to do this numerous times. Here is the best way to do this (straight from IPSWITCH):
Start by doing a search on your computer for "original.ini" and "ws_ftp.ini". When you find these files, please open them and verify that your site information is listed. If so, you will want to copy the files from the old PC to the new PC and paste them in the appropriate directory (see below for options).
In version 2006 (thru 12.2), there is an option, Import Sites, in the Tools menu. Use the table below to determine where your site profiles are kept. Then, use the Site Import Wizard to import your sites.
On Windows2000 and on Windows XP sites are kept:
c:\documents and settings\user-name\application data\Ipswitch\Ws_ftp\Sites
If you are still not able to see your sites when you open WS_FTP, go back into the ws_ftp.ini file and be sure that there is no path after filename.
(Note: The "Application Data" folder in Windows 2000 and in XP is a hidden folder. You will need to show all Hidden files/folders in your Windows Explorer settings.)
For Example:
[MySites]
FILENAME=original.ini
NOT:
[MySites]
FILENAME=C:\WINNT\Profiles\your-name\Application Data\Ipswitch\WS_FTP\Sites\original.ini
Version 6.0-6.51
All OS
C:\Program Files\WS_FTP
Original.ini and/or ws_ftp.ini
Version 7.0-7.04
98, ME
C:\WINDOWS\Application Data\Ipswitch\WS_FTP\Sites
Original.ini and/or ws_ftp.ini
NT
C:\winnt\profiles\user-name\application data\Ipswitch\WS_FTP\Sites
2000, XP
C:\documents and settings\user-name\application data\Ipswitch\WS_FTP\Sites
Version 7.5-7.62
98, ME
C:\Program Files\Common Files\Ipswitch\WS_FTP\Sites
Original.ini and/or ws_ftp.ini
NT
C:\WINNT\Profiles\All Users\application data \Ipswitch\WS_FTP\Sites
2000, XP
C:\documents and settings\<username>\application data\Ipswitch\WS_FTP\Sites
Version 8.0-9.x, 2006, 2007, 12+
98, ME
C:\Program Files\Common Files\Ipswitch\WS_FTP\Sites or,
C:\Windows\All Users\Application Data\Ipswitch\WS_FTP\Sites Original.ini and/or ws_ftp.ini
NT
C:\WINNT\Profiles\All Users\application data \Ipswitch\WS_FTP\Sites
2000, XP, 2003
C:\documents and settings\<username>\application data\Ipswitch\WS_FTP\Sites
Vista
C:\Users\<username>\AppData\Roaming\Ipswitch\WS_FTP\Sites
Version 12.2+
Win 7, Win 8, 2008
C:\Users\<username>\AppData\Roaming\Ipswitch\WS_FTP\Sites
**NOTE**
If your sites do not exist in either original.ini or ws_ftp.ini, then you most likely created a folder to store your sites in. In this case, your sites will be stored in foldername.ini.
More information can be found here.