You need to run Nintendont from the Homebrew Channel, set your options there, and boot a game. This will generate a nincfg.bin file usable by all your titles. An alternative when building your title would be to select NO when the script asks you to autoboot, that way you have full access to the Nintendont menu. After you boot your game a nincfg.bin file will be created that all future titles will be able to see.
I made a title named Configure Nintendont with autoboot turned off with a small game like Animal Crossing just to have a title to configure Nintendont with:
a question, if the script allows .dol can not be generated with the last boot.dol of nintendont to be able to access the configuration? or it is necessary to do it with a game and not to give him self-starting

