The extras are just that...extras. They are used on some other applications most likely listed on the back of the box but not our Wranglers. Just hook up whichever ones fit your radio wiring and leave the rest hang. Don't cut them off or you may run into problems with the wiring shorting together.
What I like to do when I use those connectors is when I attach the wires on the harness to the wires on the connector provided with the new headunit, I pick up some shrink tubing and solder them. Put the shrink tubing on first, solder the wires together, slide the shrink tubing over the new joint and hit it with a heat gun (or if you're careful, you can use the solder iron). Makes for a very clean install and makes sure all your wire connections are good and tight.