Thank you for the advice.
It seems like the best way is to use some kind of envelope on each track. Playing around with the noise gate works for some situations but find myself have to adjust things manually anyway when sound goes above the noise gate when one person starts talking really loud and the other microphone picks it up more or one person is making some kind of noise like moving papers, slight cough, scratch their clothing, etc.
Just got done editing a few hours of audio and video and using a new method that is speeding up the process. Right now I am keeping the audio track in stereo from the main camera with the mic feeds and using a pan envelope to go back and forth between each person with one person on the left track and the other person on the right. This allows me to easily adjust which microphone I want the sound coming from and put the pan in the center if they are talking over each other.
Using this method I only have to adjust one envelope instead of two envelopes if I had them on separate tracks and allows for smoothing transitions between each person when cutting back and forth.
From there in my audio chain I am using a free VST plugin called RS Balance Pro that allows you to take a stereo signal and send them both to the right and left track with volume controls to balance each person out and mix it down to mono. After that I use the Wave Hammer plugin to level out the signal even more and go through the Izotope Denoiser plugin to get rid of any constant background noise.
Seems to work good but would be interested in other methods that people may use.