The USB plug is how you will need to program and debug your code. We use it to both power your project and also provide the USB serial interface. On older Metro Mini's we used a FT231X chip. On newer Metro Mini's we now have the CP2104 chip. Both act the same but the CP2104 is a little less expensive so we were able to lower the price. For either one, you'll need to install drivers if you are using Mac or Windows. Linux comes with both drivers already.
To summarize, the differences between the response time runs and the stimulus timing runs are as follows. The serial port code for the TTL was only needed in the stimulus timing run (because the response timing was based on the visual stimulus it was unnecessary). The sound stimulus was also only needed in the stimulus timing run (again, it was unnecessary in the response timing run). Conversely, the keyboard checks were typically only needed in the response timing run and were omitted from the stimulus timing run.