I believe that it depends on the Gamecube loader that you are running the games through (since CFG USB is just a frontend and junk). If you are using Nintendont, it can automatically switch discs when it needs to. I think that Dios Mios does the same as well. However, I'm not too sure that CFG USB can select which disc to boot. I use USB loader GX, so I don't know too much about CFG, ah.
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