Final Cut Pro X multiple audio channels auto muting I have a recording with two audio channels, one is a lapel mic for my audio and the other is someone else sitting across the table from me (we do this because we're recording in a fairly echoey room so a single mic in the middle would sound echoey and I wasn't sure that there was an easy way to solve that and thought this would do...).

The problem I have is that I can be heard on the other mic and vice versa to a lesser extent, and when I add both audio channel to the video this slight alignment issue then recreates the echoey effect, is there a way to get FCPX to automatically mute one audio channel when the first is louder?

Or is there a better way in software of handling this that I'm missing (aside from better kit/soundproofing or moving one person to another room, the only one of which I could possibly do there is mayb slightly better microphones)
To my knowledge, there is no feature or even a plugin what can monitor one audio channel and adjust another. I would see that as it is the job of the editor or sound engineer. That's the reason you get paid the big bucks I guess. 

Better microphones definitely can help. If you get microphones which have a very distinct range you can limit the echo effect. You might consider asking in sound engineer group what microphone would be best for your situation.