WiiFlow doesn't boot Gamecube games. It has to use an external loader like Devolution, DIOS MIOS or Nintendont. I'm not completely sure how the first two handle it (I think pressing eject on the Wii swaps discs) but Nintendont handles it automatically. You just have to make sure the disc images are named properly and in the same folder. Disc 1 should be "game.iso" and disc 2 should be "disc2.iso".