You set it up on a game by game basis now, or you can just make one "general" one that works for every game. It's designed that way so that you can personally apply different PP shaders to different games in a way that best matches their visuals.
If you want a general one
edit the post.fx file in the *GeDoSaTo*\assets folder with whatever shader you'd like to apply and that post processing will apply to every game.
If you want specific ones per game
add the game to your whitelist, and create a folder in the *GeDoSaTo*\config folder that is identical to your games executable name, minus the exe.
ex: RE5DX9.exe would be RE5DX9
Once that folder is created, you can add a post.fx file to that folder and have post processing that applies specifically to that game and allows you to create custom post.fx files per game.
If you want the exact same post processing as Dark Souls II to apply to every game
Take the post.fx file from the *GeDosaTo*\config\DarkSoulsII folder and place it in the *GeDoSaTo*\assets folder
And of course, make sure that you enable post processing in the GeDoSaTo.ini file as well.
I might love GeDoSaTo more for the other features? What started out as a fairly barebones tool has become really well fleshed out with a lot of great options. The downsampling just feels like one that's part of a vast many at this point.