Both guilds must have a rating of 1,200 or higher for the battle to count towards the Champion title track. A GvG match is fought by 
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two different guilds and there are multiple types. There are rated matches that affect the official Guild Wars Ladder, unrated matches just for fun, unrated scrimmages, and Guild Wars tournaments in the game. Make sure that the GvG match is a rated match for the Champion title track.
The GvG battles will occur in the Guild Islands. When choosing a guild hall the guild leader is also choosing the location of all future GvG battles in his or her guild. Wander around your guild hall and familiarize yourself with the flag locations, resurrection shrine locations, and other important information for battle. Whatever guild in the battle has the highest rank will be the attacker and the other guild plays in their hall.