Factory radio replacement with after market radio

I went to replace my radio, i ordered a new install kit that came with the new face and some wires. i took out the old radio and something very interesting caught my attention. there was no antenna wire connected to the radio, i finally found the radio antenna connected to a box in my trunk that fed to my radio using standard wires. not 100% sure why it is set up like this but my question is do they sell install kits that will connect the new radios set up (antenna and harness seprate) to the old radio set up (antenna and harness together). or am i going to have to run a new antenna wire from my trunk to my radio?