Unfortunately, nothing is standard. So I would say, across all the configs you looked at, which had a file and module structure that you understood? I'd follow that then.
My config has a users and hosts dir, to distinguish home manager and nixos configs. Inside each is the list of users and hosts configuration files. In addition, there is a modules folder that holds modules that are common among different users/hosts.
There are no established conventions yet, you can do as you please. There are some frameworks trying to create structures, but they are in no way mandatory or even agreed upon.
i took the structure from vimjoyer's video on this. i think it's a great starting point, after which you can start experimenting with moving stuff around and borrowing from other configs as you learn how things work
how you separate modules is really up to you; i wouldn't overthink it too much. in my config, my modules are split into home-manager modules and system modules, like this:
then in those, i separate based either on subject (like shell stuff, music software, games) or if the config for one program is getting really big (like my alacritty or firefox configs). my layout evolved over a few months, so don't feel as though you need to get it spot-on from the start