There is a really neat trick to chagne location of two most important configuration files in Ghisler’s Total Commander, which is bmho the best file (& more) manager available for Windows platform. Those two files are wincmd.ini - which stores main configuration data - and wxc_ftp.ini - which stores all your FTP accounts and passwords as well. In order to launch Total Commander with specifiying your own custom locations of those two ini files, you just have to change the shortcut to main EXE file to something like this:
C:\totalcmd\TOTALCMD.EXE /i=D:/DOCS/wincmd.ini /f=D:/DOCS/wcx_ftp.ini
Switch /i defines location of wincmd.ini and, and accordingly, switch /f defines location of wxc_ftp.ini file. The path and the filename could be altered to whatever you prefer.