Make sure that on your cam you have ch1 selected for ch1 and ch2 selected for ch2... it's possible to set both mics to ch2 and then you can't seperate 'em.
So now that you've established that each mic is going to it's respective channel you can seperate 'em IN POST.
After you've loaded your audio and/or video into your NLE you can copy and paste the soundtrack to another audio track within the NLE... then duplicate LEFT on track 1 and duplicate RIGHT on track 2. There... seperated.