Things to know when creating an 'empty' (or any) Main campaign mod:
1) Make sure that Main is checked as a dependency in both boxes when creating the new module
2) After loading any random level, make sure that in the Module -> Module Settings that the Start Level is set to Character Creation, and the Menu screen is set to one of the Menuscreen (Menuscreen_Cyseal)
That being said, getting changes to stick in-game depends on where you are saving your changed file to. What file path is your changed file in?