Go to Song > Song Setup > Audio I/O Setup > Outputs
Make sure your Output for MAIN are set to Stereo L/R for the 1/2 channels, they are probably on 3/4, might even be 2 mono outputs on 3/4. Make sure all these are set up how you want (either stereo or mono). Then click the "Make Default" if you want this configuration to automatically be used for every new song you create.