Discovery is warning you to NOT use it for managing system packages , and use it ONLY to manage flatpaks and snaps. Unseeing this warning may cause you to have problems.
Best course of action is to use Bauh or Octopi.
Personally I find Bauh to be a very good and simple GUI package manager frontend, better than Octopi IMO.
For updating you can use garuda-update as recommended by @dr460nf1r3