Very exciting! You're layout looks fine as is. As it grows it might change, but for what you have now its a great schema.
On themes: catppuccin has a dedicated flake for applying the catppuccin style to a lot of different terminal apps and gnome/kde I think. I prefer this over stylix, a general purpose themer, because I want explicit control over which color scheme is enabled on each app. Stylix is cool, but doesnt make it easy (or possible?) to apply different themes to different apps.
Declarative flatpak by ~~germanbread~~ in-a-dil-emma is a nice flake. Occassionally theres a flatpak I need that isnt already packaged. This takes care of that. https://github.com/in-a-dil-emma/declarative-flatpak
If you want to work with secrets, look into sops-nix. Vimjoyer on youtube has a great video on how to get it setup.