Multiplexing is turning the LEDs on an off rapidly so they look like they are on all the time. This way you drastically cut down on the number of lines you need to control them. See
http://www.thebox.myzen.co.uk/Workshop/LED_Matrix.html
Start off with something simpler say a 3 by 3 by 3 cube and try and understand what is happening, this is far more usefull than just building what some one else has done. This is an education project. Are you going to be educated as a designer or just learn how to follow a drawing like a solder monkey?