By default FileZilla saves all its configuration files including Site Manager configuration somewhere in OS user home directory. This can be easily changed where ever you want all you have to do is to copy fzdefaults.xml.example form {FileZilla install directory}/docs and place it in:
- for Windows users in same directory as filezilla.exe
- for OSX user in Contents/SharedSupport/ subdirectory
- for Linux or BSD users in ~/.filezilla or /etc/filezilla or share/filezilla subdirectory of the install prefix
Rename copied file to fzdefaults.xml open it and change Config Location property to location where you want to save your passwords.