In a large bowl toss together cheeses and flour.
To a 4-quart saucepan, add the beer, smashed garlic and chipotle chiles and bring to a simmer for 10 minutes.
Whisk in cheese by the handful, making sure each addition melts before you add the next. Keep at a bare simmer. Transfer to a fondue pot and set over a low flame.
Serve with fondue accompaniments of fruits, vegetables and bread.
If sauce is too thick, add more beer. If it's too thin, add more cheese