You have to run wires and an antenna extension cable to the trunk because that is where the "brain" of the factory radio is located. It's mounted in the left rear side of the trunk behind the trunk liner material. Here is a link to a few pics:http://www.crutchfield.com/App/Car/outfitmycar/car.aspx
The factory radio is only a control head that supplies input signal and radio/source function switching to the radio brain. The speaker outputs and power wires all have to be routed from the brain up to the dash location to wire in to a new aftermarket deck. It also takes a specialized installation kit for the new deck in the dash, usually you can get the dash kit, antenna extension and a speaker/power wire kit for about $80.00 or $90.00. I would say call Crutchfield, Sonic Electrinix or maybe a good independent car audio shop to be sure you get the right parts and help with the installation.
2001 Dodge Dakota, 3.9 V6, 5-speed manual, 171K
Peak 10W30, Fram PH16