Yes, any multichannel audio in FCPX can be set to individual mono channels. If the Beechtek actually recording a multichannel file? I think it only has two inputs, so you can only get two channels. Then you're locked in to two channels. I don't think that unit will do more than two channel audio for you. Especially if your camera only records two channels.
From what I can find about that unit, it should be passing left channel to the camera's left channel, and right channel to the camera's right channel. Be sure it is set to stereo and not mono. No reason it shouldn't work correctly to give you two channels for two different mics.
If you use 3 mics, you need to get a recorder that has 3 mic inputs, and can record to three discreet channels. You will NOT get that by recording to a camera (most all have only 2 channels).
I use a WoodenCamera.com "A-Box" and love it. Compact, minimal, does the job with my Audio-Technical wireless system. I am rigged to to 2 wireless mics (las, hand-held, boom, whatever) to each of two cameras, total of 4 independent channels. Rarely do more than 1 or 2 mics, though.