You are correct. You need to change the theme to what you want and then install menuhax and change the type to autoboot unless a button is held (you currently have type 1, boot when a button is pressed). Unlinking your bands will solve those issues.
about themes: I used homebrew CHMM, but it installed into sysnand, and my menuhax got broken, so I searched for themes, and made my own cia using this tool: https://gbatemp.net/threads/release...kages-with-custom-and-official-themes.401081/
You need to choose your own region, up to max. 100 themes. Then simply install it on emunand with FBI. Your theme management will recognize the themes, and you can choose 10 themes to randomize.