You have successfully managed to paste in simple english as to how a 16 channel analog input stage works in the differential mode. Good.

The list of questions generally did indicate that this is your first exposure to the MCU stuff.

But this really put the lid on : "Which pin should be GND and which should be +5 "

At this level, tackling the code for a 16 channel data logger and sending it to the PC, for storage in a neatly formatted text file, will be very daunting. Try something simpler and that after first understanding the MCU.

I am not for one moment discouraging you. But simply posting what the lecturer wants you to do and expecting the full project to be completed by others, is bad for you. You learn NOTHING in the process.

Select a small simple project. Start the design on it. Come back with specific doubts. Help will flow like water out of dam.

Raghu