instantOS has an "it just works" philosophy so it shouldn't be necessary to change large parts of it. It is recommended to learn the default keybindings and how to use the OS with the default setup before changing it.
The control panel can be opened by Super+Left clicking on the status text, with Super+Ctrl+C, from the start menu or by typing instantsettings in the terminal.
You might prefer not using the included settings manager and would rather hack together your own setup. The dotfiles setting opens up a config file in vim. Here you can manage which dotfiles are managed and updated by instantOS and which can be manually edited. The instantOS section also allows disabling the management for all dotfiles and disabling the built in theming.
Lots of themes are managed by instantOS. This includes Gtk, Qt, Terminal colors, rofi (application launcher) and dunst (notification daemon). This enables things like automatically switching to a dark mode at night. You can disable all theme management in the appearance section of the settings panel. After doing that, you can set up your own themes for all of the above applications
instantOS uses st as its terminal emulator. The colors are customized using the ~/.Xresources file. You can also roll your own st build if you want to and instantOS will use it instead of the default one as long as it's installed in /usr/local/bin
The appearance section of the control panel allows changing the Gtk theme, font, icon set and cursor.
The theming system is planned to get a rework basing it around imosid once it is stable enough. This will prevent it from ever accidentally overwriting any user customisations while not requiring to be completely disabled if the user wants to customize on a file level.