You can run multiple instances of FMLE and select different devices/stream settings in each. Just double-click FMLE, then double-click again, you'll get two windows that you can set the different configurations in.
What about audio input?
If I have one audio card can FMLE use same signal from one card for 2 instances or do I need a dual input as well?
FMLE can use the same audio device.