The PlayOnline tools for configuring a controller are located in the following directory:
..\PlayOnline\SquareEnix\FINAL FANTASY XI\ToolsUS
It is called "FINAL FANTASY XI Config"
Assuming you created a folder named "PlayOnline" for your installation. The start menu shortcuts to those applications are not created with our installer.
For issues with controller settings resetting on FFXI launch, the following link fixeds this issue:
If you're using a logitech controller with X-Input, you may have to switch that off or find the appropriate drivers to install on your computer.