I am confused why the Stemtera (https://www.sparkfun.com/products/14082) has two microcontrollers. What is the purpose and are they independent or connected?
The Uno does too and the reason for it is that its’ cheaper to have a second microcontroller programmed to act as a USB to serial bridge than it is to use a dedicated USB to serial chip. Plus you have the added flexibility of making changes to the firmware in that chip later on if problems arise.
From a software standpoint they are independent from one another but they are almost completely independent on a hardware level. The RX and TX lines from the USB to serial microcontroller are connected to the ATmega328 and there’s one more I/O pin that connects to the 328’s reset line but you could conceivably run your own code on the USB to serial uC as long as it also took care of passing serial onto the 328 as well.