Important thing regarding custom layouts is that it can be designed by our tool named FPS.KeyboardCreator
It can be found at the FPS.Input Controls installation location, with the name mentioned above.
To load custom layout into your application simply put XML layout definition file into bin/Debug/Layouts or bin/Release/Layouts folder of your working version. Also you will need to add this File into Layouts folder of your Installer project for right runtime execution and delivery to customer.
please also read this KB post on how to deploy applications on Windows Vista or Windows 7 with administrator rights.