I’m using GNOME Wayland on Fedora 39 and I don’t have the problem you describe. I just go to settings and select my keyboard layouts:
English (US, intl., with dead keys)
English (intl., with AltGr dead keys)
And everything just works. I specially like the second one because it doesn’t interfere with keybindings in games, which can be a problem in GNOME Wayland.
Oh, I think I get the issue you’re having, you can’t find the Çç character on the Linux layout 😅 I always have to explain this to people migrating from Windows, it’s AltGr+, (right Alt key plus Comma). I like this shortcut better than the Windows layout, but I understand some people might not like it. Unfortunately, I can’t answer your question, as I too don’t know how to customize the keyboard layout. I just got used to the Linux layout.