What do you mean by best. its like the shortcut question, which is the better shortcut, the one that takes less time, or takes less distance. If are specific, its easier to help.
Based on the info you have provided, I can only guess that the best way to hook up the LEDs is whatever way you might learn the most (since this is a school project). That is about as specific as can be, with the info provided.
You may want to look at one of the ambilight projects, they do something similar to what you want, you may be able to adapt to suit your needs.https://en.wikipedia.org/wiki/Ambilight