Dolby E is a pure data stream wrapped in a PCM file. FCP can be set for stereo or dual mono as long as the levels are unity and hard panned Left/Right. If you make sure FCP is not altering the signal in any way that is ideal. Do not panic if the levels show as clipping into the red. Levels must be set to zero.
Beware of monitoring as it is a full level data stream so it will be just noise into your speakers.