Single instance works fine, but a separate instance allows you to set global quality settings that are more accurate for anime: https://trash-guides.info/Sonarr/Sonarr-Quality-Settings-Fil...
So I'm also surprised why someone would configure a second instance for that
I suspect it's would still work, but haven't tried it out
Sonarr/radarr has the ability to configure multiple library roots. Those are available in a drop-down when adding a new series through the (son|rad)arr interface
This is eg /media/(anime-series|series) for me. Then I defined a rule for those paths to add an anime|lifeaction Tag.
This then controls the tracker and quality profiles, as well as language preferences etc