I may get this a bit wrong, but I need to do something similar when I record two channels on a stereo file and FC gives me a single track file.
It can be done and is easy when you know how.
Highlight the file and go to the inspector, somewhere in there ( near the bottom I think) is an option to show individual mono tracks rather than a stereo track. Choose that and you gain access to the individual channels.
This side of things isn’t very elegant in FCX but it works. I have a tendency to break the channels apart and separate them from my video clip just so I can view my audio as separate tracks because I prefer seeing everything in my timeline rather than having it all tucked away into a single does all file. I am a bit of a nay sayer about all this enforced de-cluttering that X does but once you get your head around it the workarounds are easy and become second nature even if a it annoying that they need to be done and you need to ‘unpack’ your timeline just to work it as ,you may wish.