I noticed there are two Gnd pins at the lower pin strip, and another on the upper strip. Is there a difference in their purpose?
In short, all the UNO ground pins are the same.
They are just there to make your life easier. At the end of the day, GND is GND. There is no technichal difference. Just note that is is sometimes better if you share the 3 GND ports. Overloading a port might damage it. Check the datasheet for current limitations of the pins.
The pins (literal pins of the IC) themselves are also different on the ATmega IC.