You'd need to combine some mic signals prior to hitting TONEX.
For instance, Reaper has a virtual audio interface/driver called ReaRoute. You could use that, sum up the mics in Reaper, then output via ReaRoute. Then in TONEX, use ReaRoute as your audio inputs.
Other loopback/virtual audio driver software could do that. Additionally, you could of course sum in hardware using a mixer. An RME interface with TotalMix could also sum up signals. Lots of ways to do it right now without changes to TONEX.
The most important piece is getting the mics in phase. Getting 2 in phase and sounding good is hard enough.