PINE64

Newbie question here, running bog standard Manjaro:

What's the difference between the Discover app, which tells me I am to date, and pacman -Syu which goes and does a set of updates?

Pacman is the actual native package manager, I believe that Discover is a Flatpak or Snapd type of package manager, which is not native to the system you're using at all, and it's best to refrain from using those, since while it does have some newbie-friendly advantages, the disadvantages do outweight them all.
Plus if you already use Manjaro or some other Arch-based distribution (or Arch itself), Pacman should already be the easiest to use anyway, plus you can use it over SSH as well.

Thanks!