Short answer: pamac (GUI and CLI)
I’ve seen it mentioned in the forum too, and scratched my head. When I first started using Manjaro, and learning the ropes, the choice for package manager was trial and error, but I feel very confident in my choice now.
I know people that just use pamac. I use pacman (and pacman-mirrors) and pamac for the AUR. Manjaro appears to be putting a lot of effort into pamac and improving it. imho, if one is using Manjaro, pamac would be my recommendations. And when pamac hiccups, use pacman.
Most distributions have supported software and unsupported software (for your convenience, provided by another community), or some way for the user to build/compile other software. I like to think of the AUR warnings, as a reminder, like be careful of using electrical gadgets next to water. You can use them, just be careful, and all responsibility is yours.
I found this @philm entry helpful:
This is head-scratcher, too. You can do updates with pamac, but we recommend doing it in a TTY.
I update software in a GUI, but I always reboot. It takes seconds, it reduces the chance of a problem, and if there is a problem I’ll catch it earlier than later.
▼ freetype2 update might result in font characters becoming squares
Don’t worry, a relogin to your UI should fix it. We recommend to do the update in a TTY. Affected UIs so far: Gnome, Phosh, Cinnamon.
A package manager that I haven’t seen mentioned in the forum for awhile, although I’m not look’n either 
, is octopi. It’s in the Arch AUR and Manjaro promoted it to the Manjaro Community repo.