I assume you mean you have an inbound stereo stream with one language on the left and one language on the right ?
If this is the case then you set up the transcoder have to two encode blocks. Each block can have the same video settings but in the audio section you could add a parameter into the audio parameters section,
0: Do nothing (default value).
1: Copy left channel over right channel.
2: Copy right channel over left channel.
An example is the following audio section of an Encode section
This would copy the left channel over the right so the output , although would be stereo would in fact be just the left channel from the original.
<!-- AAC, PassThru, Disable -->
Hope this makes sense. You would need to add the parameter manually to your transcoder template as I dont think this can currently be done in the Manager.