if you are using the mic input to speakers you're routing a mono signal to stereo (left and right) output channels. the mono signal will be identical on the left and right speakers.
if you use the line level input you'll have a true stereo input where the left and right channel data can be different (like most recordings). you can acquire data from just 1 channel (left or right it doesn't matter as long as your signal is present on that line), you just won't have a true stereo output. for a school project it shouldn't be too critical.
as far as NIOS versus RTL it depends on your own strengths and style and what you're trying to accomplish.