Hi,
When you are using a Plug'n play module (when at least one plug'n play is activated) Atomic is in Plug'n Play mode.
It means it will only load module activated in the PlugnPlay manager other config file will be ignored.
But there 2 solutions :
1- the first one you disable all plug'n play module with the PlugnplayManager.exe , in that case Atomic will run the normal configuration you defined as start up config.
2- Using the plugnplay manager , you can add your own config file to the Module list.
If you used the multiconf wizard to create your config , you will have to add the Main.Cfg file in the module list.
But if what you are trying to do is to modify the module arcade to have the category list , it is different. Module haven't be designed to be modified in they structure, but of it is doable. Using the multiconf wizard you can generate your config based on the Arcade.cfg file , then you can edit the file Arcade.pnp (in the PlugnPlay folder) to make it point to the Main.cfg you just generated. It should work.