@servimo, this flatpak / snaps runtimes are not managed by pacman / pamac. They are managed by flatpak and snap clients. So you will not have conflicts with pacman upgrading them with fpakman.
You can check / uncheck updates by clicking the green circle located in the right corner of the app row. If the circle is hidden means the app has no update available. In Snaps case, the snapd automatically upgrades your apps, but there is a "Refresh" option when you right click a snap application that can force an update.
If your search returns nothing, click the "Refresh" button to return to the main window.