You need to use Citra so it can fill the log. It opens Citra without that other window since it’ll all get written in the log file.
And wait, I found some info regarding Inazuma Eleven Go: Chrono Stones. Actually, you need to connect with someone that has a copy of this game but the other version, just like Pokemon.
You can also connect two separate instances of Citra, one with a different version of the game open in it (Wildfire or Thunderflash). Just set your name different in one of the instances, and connect them to the same server.