This is just like a normal brawl. With the difference of guilds being matched differently based on activity rather than personal tiers instead guild upgrades are also considered. See matchmaking guilds .
When a new guild or no guild run during war sessions were made they must join the guild warfare with a panel that pops up.
After hitting join now an alert will pop up.
It won't alert when a guild is found and normally a refresh is needed best check in a few hours.