You'll definitely want a dock for your iPod that goes into the amp. This is the one that I currently use, but at an amazing price that I just saw on a deal site:
http://www.onsale.com/shop/detail~dpno~564547~descr~Kensington-Stereo+Dock+for+iPod.aspx
It works amazing, doesn't use the headphone jack, and has a remote. The only tricky thing is that when you first plug it in you have to use the remote (not the ipod or the amp) to turn the volume all the up for the the output of the dock.
If your music is encoded at a high enough bitrate, you will enjoy this immensely.