If you want free software try audacity. It is simple and supports multi-track layers as you described. It is a simple tool yet it can be very powerful, I haven't tested it but I wouldn't be suprised if it could import .aud files. It can be found here: click here
If you are thinking to spend a bit of money to get something more, I would recommend adobe auditon click here it is, in my opinion, the best around at the moment.