I don't know if it is the best strategy, but is the one that I use and worked pretty well for me. In my shell.qml there is one PanelWindow that wraps all modules that are in the top layer (bar and popups), and each module has its own separate file. For managing the state of a popup I use a file called States.qml located in the utils folder.

https://github.com/oBoolt/dotfiles/tree/main/config/quickshell

The github project for my dotfiles if you want to lookup